Andre-Pierre Gignac's first-half opener was cancelled out by Arthur Masuaku, but Florian Thauvin got what proved to be the clinching goal after the hour mark.
The win lifts OM back up to fifth place in the table, two points behind Saint-Etienne in fourth and six points behind Lille in the third and final Champions League spot.
The always volatile relationship between Marseille's fans and the team has been especially strained recently since OM were beaten 5-4 at home by Nice in the Coupe de France and then lost at Monaco at the weekend.
There were therefore vast swathes of empty seats at the Stade Velodrome for a game that was originally postponed on 18 January due to a waterlogged pitch.
Jose Anigo's side took the lead on 32 minutes when Gignac pounced on a poor backpass by Eloge Enza Yamissi before rounding 'keeper Nicolas Penneteau to score.
It was Gignac's tenth goal in the league this season and his tenth in nine games in all competitions.
Valenciennes were level before the interval as Masuaku's miscued cross from the left surprised OM goalkeeper Steve Mandanda and went into the net at the near post.
However, the hosts restored their lead in the second half when Mathieu Valbuena supplied Thauvin, whose left-footed strike from just inside the area had enough power to beat Penneteau.
Marseille held on to take all three points, although Mandanda had to make a great save to keep out a Majeed Waris header in the final seconds of stoppage time, as Valenciennes slumped to a first defeat in four in the league to remain in the relegation zone.