He has played in Mexico since 13 August 2005, when he joined Cruz Azul, scoring 4 goals against Tecos UAG in his debut match. He later joined C.F. Pachuca. In May 2006, after a successful campaign with Pachuca, he re-signed with Cruz Azul to a 2-year contract.
On 3 January 2008 he has been transferred to Cruz Azul's Rival Club América for US$1,250,000 in 2-year contract worth $700,000 annually. Núñez already wanted to leave Cruz Azul because his future in Cruz Azul depended on what would happen with the transfer of Cesar Delgado.
He played his last game for América in 2008 Copa Libertadores semi-finals first leg. He did not played the second leg due to illness and started his holiday from 4 to 24 June.
On 6 June 2008 he was put in the transfers list in Club América. Nuñez was to stay at Club América as a punishment but without playing any tournament or filial teams for not accepting to go to Puebla. However, Nuñez unilaterally terminated his contract and left for Peñarol in September 2008, after FIFA granted the player had rights to sign a new club independently to the contract dispute with América. Also, América sued Nuñez for damages after AWOL (since 25 June) on 13 August directly to FIFA and he counter-sued the club for un-paid wages of August and to resolute the contract as the club allegedly prevented him to train with club through phone conversation. On 5 February 2010, FIFA Dispute Resolution Chamber returned the case to Mexican Football Federation. In July 2010, Núñez reached an agreement with Club América.