Deportivo Cali's first game in the Colombian professional league was a defeat against Junior in Barranquilla by a 2–0 score, and their first match at home was a 2–2 draw against Deportes Caldas.

[6] With them, Deportivo Cali went on to establish a 18-match unbeaten streak in the 1949 league championship which allowed them to end up tied in points with Millonarios, forcing a tiebreaker final series to decide the champion.

Since this withdrawal was made without prior notice to Dimayor and with the club still owing money to the governing body, Deportivo Cali's affiliation (ficha) was revoked and its players were released.

[9] With that authorization, Alex Gorayeb appointed Alberto Bitar and Jorge González as Deportivo Cali's delegates to the Assembly of Dimayor held at the end of 1958, although without voice or vote.

The Dimayor executives, led by José Chalela as president, were greatly interested in the return of Deportivo Cali, given the crisis and disappearances of several clubs at the time, but a ruling issued in previous years stated that no city could have more than two teams in the league, meaning that for Deportivo Cali to rejoin the league, it would be needed that at least one of Boca Juniors or América did not participate in the tournament.

The executives led by Gorayeb refounded the club as Asociación Deportivo Cali, paid the debts still held with Dimayor and formed a team to participate in the league championship.

For that campaign, the Argentine Francisco "Pancho" Villegas arrived as manager after coaching Cúcuta Deportivo in the previous season, along with players such as Iroldo Rodríguez, Jorge Ramírez Gallego, Óscar López, Joaquín Sánchez, Bernardo "Cunda" Valencia, among others.

However, they were able to stage a comeback during the second half of the season which allowed them to take the lead ahead of the final stretch, moving three points clear of Deportivo Pereira.

With this Deportivo Cali became one of the top teams from the Colombian national league, along with Bogotá sides Millonarios and Santa Fe which had won most of the championships played until then.

Similar to Valderrama, Arboleda used a variety of skill and "magic" that left opponents lost and beaten, which gave rise to his nickname "El Maestro" (The Master).

[15] In the 1975 Copa Libertadores, Deportivo Cali claimed its first victories against Brazilian teams in the competition, defeating Cruzeiro and Vasco da Gama at home, although that was not enough to reach the semifinal stage of the tournament,[16] whilst in the 1977 edition of the continental tournament they won a first stage group that also involved Atlético Nacional as well as Bolivian sides Bolívar and Oriente Petrolero, but ended second to the eventual champions Boca Juniors in their semifinal group.

[2] In the finals they faced the defending champions Boca Juniors, ultimately losing the series after a scoreless draw at home and a 4–0 defeat at La Bombonera.

[18] Whilst Deportivo Cali achieved yet another runner-up finish in 1980, and claimed an iconic win against River Plate at Estadio Monumental in the 1981 Copa Libertadores which knocked the Argentine side out of the competition,[19] the decade of the 1980s saw the accentuation of the club's relative decline in the Colombian football panorama, as well as the emergence and consolidation of América de Cali and Atlético Nacional as Colombian football powers.

However, the team's performance declined in the final stretch, after drawing with Atlético Bucaramanga, Junior, and Millonarios, and losing a critical derby to América.

Although the team began the final stages with a loss to Millonarios in Bogotá, they bounced back with four straight wins against Once Caldas, Nacional, Quindío and Junior, streak that was cut after losing 2–1 to América.

[21] Deportivo Cali and América also had an intense head-to-head in the 1987 Copa Libertadores, tying for first place in their group with 8 points and the same number of goals scored and conceded.

[22] The key players for Deportivo Cali at the time were Carlos "El Pibe" Valderrama and Bernardo Redín, none of whom was able to win a title with the club.

Cheché, who was managing a team for the first time, replaced Reinaldo Rueda at the helm after he left midway into the season due to Cali's subpar performances, and managed to stage a comeback that allowed the team to advance to the semi-finals after finishing eighth in the Finalización tournament, and later went on to win a semi-final group that once again featured Atlético Nacional, Millonarios, and América de Cali as rivals.

After eliminating Colo-Colo in the round of 16, Uruguayan side Bella Vista in the quarter-finals and Cerro Porteño in the semi-finals, they reached the final of the competition for the second time in history.

[27] Venezuelan goalkeeper Rafael Dudamel, defenders Hernán Gaviria, Mario Yepes, and Gerardo Bedoya, and midfielders Arley Betancourt, Mayer Candelo, and Martín Zapata were some of the most important players of the club in both the 1998 national championship and the Copa Libertadores run the following year.

[29] At the time, the team was leading the 2002 Finalización and was heavily favored to win the title but was unable to recover from this event and ended in second place of its semifinal group, behind eventual champions Independiente Medellín.

In 2010, Deportivo Cali failed to qualify for the final rounds of both the Apertura and the Finalización, but was able to win the Copa Colombia for the first time in history under the management of Jaime de la Pava.

Los Azucareros managed to win their regional group and then defeated Junior, Santa Fe, and La Equidad in their run to the final, where they faced surprise package Itagüí Ditaires.

[30] In the 2011 Apertura, and despite having one of their worst starts in history by losing the first four games of the season, Deportivo Cali managed to make it to the quarterfinals, where they were eliminated in a penalty shoot-out by eventual champions Atlético Nacional in a match that could have gone either way.

Deportivo Cali also competed in the 2011 Copa Sudamericana but were knocked out by Santa Fe on penalties, while in the Torneo Finalización they were unable to qualify for the semifinals.

Other notable young player in the campaign was 22-year old Andrés Felipe Roa, who scored Deportivo Cali's deciding goal in the league finals against Independiente Medellín and was called up for the senior team and also played the Olympic Games play-off against United States along with his fellow mates Luis Manuel Orejuela and Kevin Balanta.

Their Finalización campaign started with a 2–1 away victory against Santa Fe, however, a subsequent string of poor results caused the dismissal of manager Alfredo Arias midway into the tournament.

However, the team's performance improved, and a winning streak of four matches in the final stretch of the first stage helped them qualify for the semi-finals in seventh place.

[40] Although the rise and consolidation of Atlético Nacional and América de Cali starting from the 1980s has caused interest in this rivalry to decline somewhat, it is still considered an important match in Colombian football.

Founded in 2019, the club is one of four to have won the Colombian women's football league, winning the title in 2021 and 2024, as well as having one runner-up finish in 2022,[46] and placing fourth at the 2022 Copa Libertadores Femenina.