Rennes started the final day in fifth spot, with a three-point advantage over Marseille and with an outside chance of snatching a top-four finish.
However, any hopes of clinching UEFA Champions League qualification were effectively quashed by a disastrous opening 10 minutes at the Stade Vélodrome.
Pierre-Emile Højbjerg required just two minutes to score his fourth Ligue 1 goal of the season, slotting a low shot beyond Mathys Silistrie.
Matters quickly got worse for Rennes when the determined Amine Gouiri charged down Silistrie’s clearance to force the ball into the awaiting net.
After being left dazed by their sluggish start, Rennes eventually offered an attacking threat midway through the first period when Ludovic Blas forced Gerónimo Rulli into a near-post stop.
The Marseille goalkeeper was then required to make a much tougher stop to keep out Musa Al-Taamari's curling effort from distance, reacting smartly to tip the ball onto the crossbar.
After being reminded of the visitor's threat, Habib Beye, who was sacked by Rennes in February, would have been delighted to see Pierre-Emerick Aubameyang extend his team’s lead in the opening stages of the second period.
A move that started with Rennes carelessly losing possession culminated with Aubameyang sending an inch-perfect chip in at the far post.
As the game entered the closing stages, Esteban Lepaul proved why he is Ligue 1’s top scorer, rising high to steer a header home from Arnaud Nordin’s clipped cross, just minutes after Mahdi Camara had struck the woodwork.
Lepaul’s 21st league goal gave Franck Haise’s charges some late impetus, but it could not stop them from falling to a defeat that will send them to the Conference League, unless Lens beat Nice in the Coupe de France final to convert sixth place into a UEL spot.
Flashscore Man of the Match: Pierre-Emile Højbjerg (Marseille)