Jorge Sampaoli's side bounced back from their 2-0 defeat to Colombia's Nacional last week with an emphatic win at the Estadio Santa Laura in Group Eight.
Fernandes scored his first in the 29th minute after being set up by Eugenio Mena and Gustavo Lorenzetti widened the gap five minutes later. Seconds before the half-time whistle, Fernandes headed in a Lorenzetti cross to make it 3-0.
Leonardo Sigali gave Godoy Cruz hope by reducing the deficit in the 53rd minute but Fernandes made it 4-1 in the 73rd before Angelo Henriquez tucker away Mena's pass in injury time.
It was the first win in the group stage for Universidad de Chile, who won the Copa Sudamericana three months ago.
Sampaoli told reporters in Santiago: "The team created 21 goalscoring opportunities and scored five. The gap could have been even wider.
"It was a very solid performance and it gives us a chance to qualify. We played much better than in a lot of matches in the Copa Sudamericana last year. We expected the team would play this way. It was one of our best performances."
Argentina's Velez Sarsfield battled to defeat Mexican giants Guadalajara 3-0 in Buenos Aires.
It was not until the 67th minute that Velez broke through the Guadalajara defence, as Mauro Obolo beat Luis Michel to open the scoring.
Guadalajara pressed for an equaliser but Federico Insua contributed a brace to ensure the win for Ricardo Gareca's Velez Sarsfield.
In the 81st minute, Obolo set up Insua after a defensive mistake by Guadalajara, and Insua scored again two minutes later from Lucas Pratto's pass.
Insua told Fox Sports: "It was difficult because Guadalajara played very well. In the first half, we put pressure on them and had some opportunities to score. In the second half, we made the difference."