After retiring as a player, in 1995 Gómez initially became Héctor Cúper's assistant at Club Atlético Lanús, and when Cúper left to join Mallorca in Spain, Gómez took over as manager and surprisingly led the club to its second Copa CONMEBOL final in a row, eventually losing to Atlético Mineiro.
[4] In December 2004, he took over at Gimnasia y Esgrima de Jujuy, guiding them to the 2nd place in the 2nd division and consequent promotion to Primera División.
On 9 March 2010, Last-place Club Atlético Tucumán officials sacked Osvaldo Sosa and replaced him with the former Asteras Tripolis coach.
In 2013, Gómez was confirmed as the new coach of Ecuador's Deportivo Cuenca, managing to win the 2014 Lunar New Year Cup in Hong Kong.
At the end of 2014, South China convener Wallace Cheung announced that Mario Gómez has taken over as the club's new manager, replacing Yeung Ching Kwong.
[8] In November 2017, Persib Bandung confirmed sign Gómez to be the head coach, who have been searching for a long-term replacement for Djajang Nurdjaman.
[12] Ferro Carril Oeste Lanús Gymnasia y Esgrima de Jujuy Deportivo Cuenca Johor Darul Ta'zim