The project has faced criticisms from some people because of the impact it would have on the World Heritage Site.
The final chance of the match fell to Madrid's Tony Kroos but the German's effort went wide.
The Belgian then played a major role in the second goal in the 33rd minute, setting up Raheem Sterling, whose ball into space was put into the empty net from 10 yards by Phil Foden.
Tokyo 2020 President Mori Yoshiro added: "We will continue to work hard on simplifications towards next year and ask for the continued cooperation of all those involved in the Games." Enditem
In Sunday's game, Pirlo started new arrivals Dejan Kulusevski and Weston McKennie, with talisman Cristiano Ronaldo leading the attacking line.
A first half goal from new signing Alvaro Negredo and an 83rd minute striker from Jorge Pombo gave Cadiz a 2-0 win away to Huesca in a duel between two newly promoted sides.
Germain's header in the 85th minute, which was set up by a corner from Morgan Sanson, avoided a second straight home defeat for last season's runners-up. Enditem
Bayern then reestablished control of the game, but Robert Lewandowski and Leroy Sane both had goals chalked off.
"It's great to play and to be back with my teammates. I return with a victory and a goal, so I am happy. We are getting our feeling back, our way of playing," the 21-year-old Mbappe said after the match.
Kulusevski put Juve in charge in the first half, while Leonardo Bonucci and Ronaldo sealed matters after the break.
Things haven't improved at all after Wagner failed to win one of last season's final 16 games. They also suffered a devastating start to the current campaign after being thrashed 8-0 by 2020 treble winner Bayern Munich.