The first leg ended 0-0 and the tie appeared to be heading for a first goalless draw after two legs in Champions League knockout history until James Rodriguez slipped a pass through to Cristiano Ronaldo in the 88th minute.
The Portugal forward unselfishly squared for Hernandez and the Mexican striker stroked the ball past Atletico goalkeeper Jan Oblak to seal a 1-0 aggregate victory, Real's first win over Atletico in eight matches this season.
It was a bitter blow for Diego Simeone's men, who went toe to toe with the team that beat them in last year's final until playmaker Arda Turan was dismissed for a second booking 14 minutes from time and Hernandez applied the killer blow.
“It was my turn to score but this is for everyone,” an emotional Hernandez, who is on loan at Real from Manchester United, told with Spanish television.
“Atletico are a worthy opponent,” added the 26-year-old, who was playing only due to an injury to Karim Benzema. “Thank God, we were the worthy winners.”
Real coach Carlo Ancelotti, missing injured regulars Gareth Bale, Benzema and Luka Modric, started with Hernandez up front with Ronaldo and centre back Sergio Ramos pushed forward into a defensive midfield role.
Seeking to become the first team to retain the trophy in the Champions League era, Real had the upper hand in terms of possession and chances in a cagey first half.
Ronaldo forced a good save from Oblak with a 32nd-minute free kick before racing through with a clear site of goal a minute before halftime.
Oblak was again equal to the challenge, racing out to block Ronaldo's fierce shot and deflect the ball away for a corner.
Real threatened immediately at the start of the second period when Isco threaded a pass through for Hernandez but he scuffed his shot wide of the far post.
Atletico hopes suffered a massive blow when Arda picked up a second yellow for a foot-up challenge on Ramos and he was distraught as he trudged off to a cacophony of whistles.
The draw for the semi-finals is on Friday, with Barcelona, Bayern Munich and Juventus joining Real in the pot. – Reuters
Original source: Hernandez ends Atletico jinx