Goals by Loic Remy, Amalfitano and Andre Ayew gave Didier Deschamps's side all three points as Marseille moved up to ninth in the standings on 21 points from 15 games while PSG, who spent more than 80 million euros in the last transfer window, stayed second on 30 points.
They trail leaders Montpellier, who claimed a 3-1 win at Sochaux on Saturday, by three points.
Marseille, who lost 1-0 at home to Olympiakos Piraeus in the Champions League on Wednesday, had an unsettling week with Deschamps sending striker Andre-Pierre Gignac to train with the reserves after a disagreement.
"We are capable of playing well. There is no reason why it should stop," Remy told French TV channel Canal Plus.
"We showed we can play great games. I was upset on Wednesday [after the Olympiakos game]. Tonight, we were good from the first to the last minute," said defender Souleymane Diawara.
PSG general manager Leonardo tried to remain upbeat.
"It's hard to lose 3-0 but it does not change anything. We played 15 matches and there are 23 left. We're at the start of our project," Leonardo told Canal Plus.
"There is always a tough moment in a season."
Marseille fans had decided not to cheer on their team after the French interior ministry banned away fans from OM v PSG clashes this season to avoid clashes between rival supporters.
A huge roar, however, broke out in the ninth minute when Remy headed home from a fine long cross by Cesar Azpilicueta.
Remy was replaced by Jordan Ayew in the 32nd minute with a possible ankle injury.
Ten minutes from the break, PSG went close as a Momo Sissoko 25-metre strike smashed Steve Mandanda's left post.
PUSHED HARDER
Marseille pushed harder in the second half as PSG lacked creativity in midfield with Argentine sensation Javier Pastore, who joined from Palermo for a French record 42 million euros last summer, looking listless.
Pastore and France striker Kevin Gameiro, who failed to muster a single shot, were replaced shortly before the hour by Mathieu Bodmer and Mevlut Erding but it made little difference.
Marseille went 2-0 up in the 65th minute when Jordan Ayew set up Amalfitano nicely on the right flank for the midfielder to beat Salvatore Sirigu with an angled low shot.
Ghana striker Andre Ayew completed the scoring seven minutes from time, netting with a downward header from an Amalfitano cross.
Earlier, Lisandro Lopez signalled his return to form with two goals as Olympique Lyon got back to winning ways with a 3-0 victory at AJ Auxerre.
Lisandro, starting a Ligue 1 game for the first time since his 12-week injury layoff, scored in each half and Michel Bastos added a third in the closing stages as Lyon remained fifth in the table.
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