The Argentina star emerged as a major target at Stamford Bridge following a successful World Cup, during which Fernandez won the coveted Young Player of the Tournament Award.
A deal, however, always looked difficult to do.
The Lisbon giants had frequently expressed their desire to keep the 21-year-old and publicly criticised Chelsea’s conduct.
While Fernandez was thought to have a release clause worth around £112m in his contract, Standard Sport understands Chelsea were aiming to pay that over a series of instalments.
Talks duly stalled and manager Roger Schmidt claimed the matter was closed, though the interest from west London continued.
Still, Fernandez himself has now appeared to confirm he will remain in the Portuguese capital.
After scoring against Varzim in the Taco de Portugal on Tuesday night, the former River Plate youngster celebrated by tapping the club’s badge before pointing at the ground to indicate he was staying.
Schmidt then revealed: “I can say that I expect Enzo Fernández to stay, so to have Enzo at the end of the market.
“I never doubted Enzo, his attitude and personality. He’s a great person, he’s at Benfica, he loves playing for Benfica.”
Chelsea are now set to complete the signing of Joao Felix and hold an interest in England pair Jude Bellingham and Declan Rice ahead of the summer transfer window.