PSG only needed a draw to secure top spot in the section and Zlatan Ibrahimovic gave them a dream start, opening the scoring inside seven minutes.
The sending-off of Marco Verratti early in the second half left the hosts down to 10 men, and Olympiakos profited from their man advantage to draw level through Kostas Manolas with nine minutes remaining.
However, Edinson Cavani's 90th-minute strike handed PSG the win as they progress while Olympiakos are left to fight it out with Benfica for the second qualifying berth in the last round of games next month after the Portuguese outfit won 3-2 away to Anderlecht.
PSG coach Laurent Blanc admitted that it was mission accomplished for his side, who will go to Benfica next month with the pressure off.
"We didn't manage to finish the job against Anderlecht (a 1-1 draw) so we wanted to do so here. There is a feeling of satisfaction for the players and the staff as we have done what we set out to do at the start of the campaign," he said.
This was a meeting of two in-form teams, with PSG defending a record of 34 games unbeaten stretching back nearly nine months and Olympiakos having lost only once this season.
However, that defeat was a 4-1 reverse at the hands of PSG when the clubs last met in Piraeus in September, so the Greek champions knew the size of the task before them at the Parc des Princes.
The encounter also brought together several of the most exciting talents in the European game just now, from Ibrahimovic and Cavani in the home ranks to Greek hotshot Kostas Mitroglou, scorer of 23 goals in 22 games this season.
But in an encounter in which both sides were in a position to seal qualification, it was Ibrahimovic and PSG who struck first just seven minutes in.
It was a textbook PSG goal, with Gregory Van der Wiel surging forward down the right and crossing low for Ibrahimovic to score his 18th goal in his last 12 games for club and country from close range.
The combination of Van der Wiel and Ibrahimovic has been one of PSG's most potent sources of goals this season, and Olympiakos coach Michel had actually started with two left-backs on the field in an attempt to stop the danger coming from the Dutchman.
Forced to open up after the concession of that goal, Olympiakos were rather enterprising, and Mitroglou nearly equalised within five minutes, Salvatore Sirigu turning his first-time shot from Joel Campbell's cross around the post.
Mitroglou tested Sirigu on two more occasions in the first half, but Cavani gave a glimpse of his menace too with a strike that required Roberto in the Olympiakos goal to make a firm-handed save.
The Ligue 1 leaders were in control at the interval, but they were dealt a serious blow less than 30 seconds after the restart.
Many spectators had not yet retaken their seats when Scottish referee Craig Thomson sent off Verratti, the young Italian - who had been cautioned for handball in the first half - picking up a second yellow for pulling back David Fuster on the halfway line.
Blanc reacted to that by taking off a forward in Ezequiel Lavezzi and reinforcing his midfield with Adrien Rabiot, and the substitute's first involvement was to win a free-kick which Ibrahimovic struck fiercely from 35 yards, forcing Roberto into action again.
The Spanish goalkeeper then denied Rabiot himself, tipping a crisp left-footed drive from the teenager around the post, and Olympiakos went on to equalise in controversial fashion.
Manolas turned the ball in after Sirigu had denied substitute Alejandro Dominguez at a corner, but Dominguez was in an offside position when he connected with the initial knockdown by Manolas, and PSG will feel justice was done after Cavani burst through to make it 2-1 at the death.
Photos: Salman Khan returns from Jodhpur to Mumbai
Pics: Sidharth Shukla-Rashami Desai's sizzling chemistry at TV show launch
Ooh La Lana! WWE Diva flaunts sexy curves in these 30 pictures
15 'peach' perfect photos of Priyanka Chopra at People's Choice Awards 2017
62 going on 16: These photos of Rekha prove she is 'forever young'