Jorge Sampaoli’s men had dropped to third behind Nice after their top-three rivals’ 0-0 draw at Strasbourg on Saturday.
Marseille are now 15 points adrift of runaway leaders Paris Saint-Germain.
OM were far from their best at Troyes, creating little but led for the majority of the match after Dimitri Payet’s 28th-minute spot-kick, which he smashed into the top corner.
But Troyes struck back in the 90th minute, substitute Yoann Touzghar netting from close range.
Marseille boss Sampaoli said the journey to Azeri capital Baku to face Qarabag in the Europa Conference League in midweek had left his team fatigued.
“For us it was a very difficult game because we were coming back from a long trip but despite everything we controlled it well,” said the Argentinian.
The point dragged Troyes from the bottom of the table to outside the relegation zone.
Elsewhere, defending champions Lille moved to within four points of the European places with a 1-0 at Lyon, who slipped to 10th.
Swedish defender Gabriel Gudmundsson scored the only goal in the first half.
Monaco’s European hopes suffered another setback with a late collapse in a 2-1 home loss to Reims, with teenager Nathanael Mbuku scoring an injury-time winner.
Bordeaux remain at the foot of the table after a 1-1 draw at fellow strugglers Clermont, while Lens moved up to sixth by winning 2-1 at Angers.
On Saturday, PSG had continued their romp towards the title with a 3-1 victory over Saint-Etienne.