As the final whistle blew — and Bayern Munich's dejected superstars slumped to the ground — Villarreal's substitutes raced onto the field to join the teammates who ousted the six-time European champions.
The veteran Spanish midfielder levelled for Villarreal in the 66th minute, leaving the playoff poised for the decider in Italy with the away-goal rule scrapped this season.
Chelsea's Champions League title defence resumes in the round of 16 with captain Cesar Azpilicueta potentially fit to return after a groin issue.
Unai Emery's Villarreal lost 2-1 at Sporting Gijon after the second-division side came from behind while Osasuna were ousted by second-division Girona 1-0
The Group F match was originally scheduled to take place on Wednesday and kickoff was initially delayed by 20 minutes before it was decided to reschedule.
The result was harsh on Villarreal who were pressing for a winning goal when a bad defensive error gifted Barca their second goal of the game late on Saturday night.
Ronaldo made his most decisive intervention with virtually the last kick of the game at Old Trafford to complete United's dramatic comeback in a 2-1 victory over Villarreal.
The draw on Saturday gave Madrid a three-point lead over Sevilla at the top of the table.
It was the seventh consecutive winless opening match for Villarreal in the league, and it hasn't started the season with a win at home in six attempts.
Less than 10 weeks after Chelsea's 1-0 win over Manchester City in the Champions League final in Porto, Cesar Azpilicueta once again lifted a European trophy to the backdrop of fireworks and tickertape.
The Manchester United goalkeeper's decisive penalty shot lacked power and was stopped by the Villarreal keeper Geronimo Rulli, who dived to his left to block the shot with comfort.
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Soundly defeating the likes of Arsenal and Salzburg on their collision course with Manchester United, Unai Emery and side are yet to lose a match in the competition and have drawn just twice.
It has been a precarious road to the road to silverware for Manchester United, who had to suffer a early group stage exit at the Champions League in order to be on collision course with Villarreal for the Europa League final.
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Emery's Villarreal held Arsenal to a 0-0 draw in the second leg of their semifinal on Thursday, which was enough to secure a 2-1 aggregate win.
Villarreal are making their fifth attempt to reach a European final, having failed on all previous occasions.
In only his second appearance of the season, striker Mariano Díaz scored a goal three minutes after kickoff in a promising start for Madrid at Villarreal’s Estadio de la Cerámica.
The Villrreal striker first cancels the Eibar goal then assists Paco Alcacer in the winning goal against Eibar.
The 19-year-old attacking midfielder played this season on loan at Mallorca, which was relegated to the second division in the Spanish league. He scored four times and had five assists in 36 matches.
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