[2] Then during the winter break of the 1998–99 season, after he had played 18 league matches and scoring six goals, he was loaned out to FC Basel.

[3] He played his domestic league debut for them one week later in the away game in the Stadion Allmend as Basel won 2–0 against Luzern.

[6] Following his six month loan, Varela returned to play for Servette during the 1999–2000 season and he had another successful time with them, 30 appearances and five goals.

[7] His contract with Servette expired and he left the club, signing a definitive transfer to FC Basel under head coach Christian Gross for their 2000–01 season and Varela immediately became regular starter with them.

Basel were able to play their home games of the championship group in their new stadium, the St. Jakob-Park which opened on 15 March 2001 and it was sold out with 33,433 spectators on three occasions.

In the second leg of the semi-final on 1 August in the Stade Olympique de la Pontaise Varela scored the equaliser as Basel drew 2–2 with Lausanne-Sport, as they won 5–2 on aggregate to advance to the final.

Basel started well into the second part of the season and during this period FCB played their best football, pulling away at the top of the table and subsequently achieved the championship title prematurely.

Basel won the last game of the season, on 8 May 2002, and became champions ten points clear at the top of the table.

They ended this in second position behind Valencia, but ahead of Liverpool and Spartak Moscow to advance to the second group stage.

Varela was also known for his emotional outbursts, this was shown again in the 2008–09 season, after just the first three games he already had three warnings and one dismissal (directly red).

Soon after the start of the 2010–11 season (four games) he received a three match ban from the Swiss Football Association for unsportsmanlike conduct against a linesman and a day later he cancelled his contract with the club and became free agent.

[16] After a lengthy trial, Varela eventually signed with D.C. United, a professional soccer club based in Washington, D.C., on 14 September 2010, but he never broke into the team.

At the end of the season they won promotion by being second position in the division and winning the play-off match 3–2 on aggregate against Bellinzona.