Genoa had stunned Juventus 3-1 at the Luigi Ferraris last September.
Real Madrid finish with 10 men after Sergio Ramos went out seeing red card.
Leipzig are eight points behind in second place with four matches left.
Rooney scores on return as United close in on City.
The final will be played on May 27.
Stefano Pioli's men suffered a dramatic collapse in the space of 17 second-half minutes.
Victory restores Atletico's three-point lead over Sevilla in the fight for third place.
They lead Monaco by three points but the principality side, who face a tricky trip to Olympique Lyonnais on Sunday, have two games in hand.
Both players are likely to miss the rest of the season.
Gaston Ramirez's sending off cost struggling Middlesbrough dear on Saturday as a 4-0 whipping by Bournemouth left them nine points shy of safety in the Premier League.
Bayern are on 70 points, with second-placed RB Leipzig on 61.
Antonio Conte's men progress to the final after late goals from Eden Hazard and Nemanja Matric sealed a 4-2 victory.
It is scheduled to open later this year and will be based at the AFC House in Kuala Lumpur.