McLaren, who have signed current Sauber driver Perez to replace Lewis Hamilton, confirmed the 22-year-old's professional link to Fernandez, 47.
Fernandez - an owner of racing teams as well - has also been backed through his career by Perez's sponsor Telmex, but Fernandez denied Perez is still a "pay driver".
"He is not bringing money to the (McLaren) team," he insisted.
Switzerland's Blick newspaper estimated Perez's new three-year contract to be worth EUR 10 million.
"I have been a successful driver and a successful team owner and now, with this, I hope I can be a successful manager and do a fantastic job for Sergio," added Fernandez.