Valencia, third in La Liga last season, were expected to face a stern test against a rejuvenated Atletico side, but showed remarkable resilience as they held on to Roberto Soldado's 53rd-minute winner.
Saturday's result was as impressive as their opening league fixture against Racing Santander two weeks ago, when two late strikes by Soldado secured a 4-3 victory.
And Hernandez believes these recent results are evidence that the Valencia side is fast gaining in maturity.
"The two victories in the league have been good for the squad, giving us confidence going into the Champions League," Hernandez told AS.
"A few seasons ago, the comeback [against Racing] would have been impossible, and against Atletico, we would not have been able to maintain the lead."
However, Hernandez admitted the win over Atletico had taken a lot out of the side, and gave credit to new Atletico signing Diego, who dictated the play after being brought on.
"We paid physically for the effort we had put into the game, and when Diego came on for Atletico, we struggled to get the ball."
Valencia next play Belgian side Genk in their opening Champions League match on Tuesday, before they look to continue their 100% record in the league when they visit Sporting Gijon on Saturday.