The England captain, who scored 44 goals across all competitions in his debut season with Bayern Munich, was replaced by Eric Maxim Choupo-Moting.
With five minutes remaining of regulation time to go, the tie was all but wrapped up with the German giants leading 1-0 on the night and 3-2 on aggregate.
Harry Kane was substituted alongside attacking midfielder Jamal Musiala, but 10 minutes earlier center-back Kim Min-jae had replaced Leroy Sane as the Germans switched to a more defensive three-man system. A brave call made by Bayern boss Tuchel, who will depart at the end of this season.
On the night, it was another striker that stole the headlines. Real substitute Joselu inspired a stunning late turnaround, scoring twice in three minutes to turn the tie on its head, and Bayern was left without their top scorer as they searched for a stoppage-time equalizer.
Indeed, Joselu has the best minutes-per-goal ratio (one goal every 54 minutes) of any player to play at least 100 minutes in the UEFA Champions League this season.
The forward went on to say that he could not have imagined this scenario: “You always dream of this kind of performance, but not even my most beautiful dreams are as big as what happened.
“I don’t know anything about being a hero, but I’m very happy. It was incredible, something spectacular. This team never gives up, it’s in its blood to fight to the end and that’s what we’ve done.”