David Fuster opened the scoring for the hosts with a header in the 22nd minute, but Simon Kroon capped off a great counter-attacking move to pull the Swedish champions level just before the hour.
Michel's charges were back in front just four minutes later with a stunning Alejandro Dominguez half-volley, but again, Malmo found themselves level with a carbon copy of their first goal, this time scored by Markus Rosenberg.
The Greek champions managed to secure the win with two goals in the last 10 minutes, courtesy of Kostas Mitroglou and Ibrahim Afellay.
However, Olympiacos had to make do with a place in the Europa League following Juventus's goalless draw with Atletico Madrid in Turin, which consigned them to third place in Group A.
Here, Sports Mole analyses the match action to determine if the hosts were worthy winners.
On target: 12
On target: 2
Was the result fair?
Very much so. Olympiacos were on top in virtually every facet of the game. They had the Swedish champions under siege at times, and over the course of the game, racked up over double the number of shots as their opponents, with over six times the number of efforts on target. That said, Malmo did well in that their only two shots on target were both converted - testament to their clinical counter-attacking abilities. However, the hosts deserved the win.
Put simply, they went out there to secure a win, and nothing but. And their performance reflected this, as they attacked at every opportunity, with passion and flair. Because of this, they left themselves exposed at the back, which allowed Malmo to cut through the open spaces and score through counter-attacks not once, but twice. Nevertheless, the old adage of outscoring the opposition worked well today for the Greek champions.
Malmo's domestic season finished two weeks ago, and indeed, some rustiness showed within the ranks of the Swedish champions, who never really got into gear all evening against opposition who were gunning for a win - except for two moments of counter-attacking genius, whereby they made the most of Olympiacos's stretched ranks to burst through the gaps and score. The visitors also resorted to very physical play as the game went on, which culminated in a multitude of bookings and a sending-off. A brave effort, but they came up short.
Sports Mole's man of the match
Alejandro Dominguez: The Argentine was a constant menace for the hosts and was the catalyst behind most of their forward play. Capped off his performance with a superb half-volleyed goal from the edge of the box with echoes of Maxi Rodriguez's strike for Argentina against Mexico in the 2006 World Cup.
Delvin Ndinga nearly gifted Malmo an equaliser in the 38th minute when he connected poorly with the ball following a long throw into the Olympiacos box, which came close to spiralling into the top corner of his own goal.
Stephane Lannoy was pretty anonymous in the game, which means that he's done a good job. He was firm enough to hand out bookings as and when needed, and was right to send off Enoch Kofi Adu by handing him a second yellow card, but apart from that, let the game flow nicely.
Olympiacos: The Greek champions travel to Levadiakos in the Super League this Saturday.
Malmo: That's it for them! The Swedish outfit have completed all their domestic league and cup fixtures, and now that their involvement in Europe is over, it's a case of looking forward to the new season for them.