Following a great season with The Students, Fernández was signed by Kaizer Chiefs from Wits University in 2001 along with midfielder Stanton Fredericks.
The big break finally came, when he made his debut in the Vodacom Challenge against Ghanaian side Hearts of Oak at Royal Bafokeng Stadium on 30 June 2001.
He had also battled to command a first team place in the same season and only got a run in the 5–0 ABSA Cup first round victory against Sporting at Ellis Park.
Fernández made his full international debut for the South Africa national team in a 2–0 win against Tunisia in August 2004.
He had hoped to be a part of his country's squad at the 2010 FIFA World Cup to be held in South Africa, but was omitted from the final 23 by coach Carlos Alberto Parreira in favour of Itumeleng Khune, Moeneeb Josephs and Shu-Aib Walters.