PSG still progressed to the round of 16 after topping Group B ahead of Bayern and there were mixed feelings for head coach Emery post-match.
Referee Cuneyt Cakir waved away the furious protest by Alves and Tolisso stayed on the pitch to help Bayern close out the win.
Bayern grew in ambition as they pressed for a second goal but the direct running and pace of Mbappe and Neymar caused them problems, the latter forcing Ulreich to turn the ball behind after he was played in by the former Monaco teenager.
"That was a good signal to our rivals", insisted midfielder Sebastian Rudy.
The 72-year-old coached Bayern to the 2013 treble and has managed the delicate balancing act of dividing up game time fairly among his star-studded squad. Meanwhile, none of the other group winners will relish the prospect of drawing this formidable Bayern side first time out in the knockout phase.
PSG president Nasser Al-Khelaifi described Bayern's performance as a "lesson for everyone".
"The game shows we are getting better, that we believe in ourselves", he said.
Boateng: It's not our objective to finish top of the group.
62 - CHANCE: Neymar finds Mbappe on the edge of the area and he reels off an excellent half-volley.
It was something Ancelotti never really got right in his 15 months at the helm. The Parisians look set for a deep run in the competition this season, but do they have the mettle to go all the way? "Changes like that are obvious to me".
Jupp Heynckes' side exploited defensive weaknesses in the French side as they finished the group stage with an impressive 3-1 win.
"Furthermore he is a very good team player, with a great engine and strong in the tackle".
"He is playing exceptionally well and he wanted the fourth or fifth goal".
And Tolisso put the result beyond doubt on 69 minutes, slamming home his second goal after taking advantage of fine work from compatriot Kingsley Coman on the left.
Bayern have scored in each of their last 63 competitive games in the Allianz Arena..
Several of the current Bayern squad won the title in 2013 and have the experience of reaching at least the semi-finals five years in a row between 2012 and 2016.