Cuisance headed home with two minutes remaining to earn Marseille their second win in their last 12 league games, three days after they were knocked out of the French Cup by amateurs Canet en Roussillon.
The win lifted Marseille up to sixth on 42 points from 28 games, 20 behind leaders Lille.
The game, initially scheduled on Jan. 30, was postponed after Marseille fans broke into the team's training centre hours before kickoff.
Since then, president Jacques-Henri Eyraud was sacked by owner Frank McCourt and coach Andre Villas-Boas, who was suspended after offering to resign, was replaced by Sampaoli.
The Argentine sat on the bench for the first time on Wednesday, 12 days after being named, after going through a quarantine period due to French government measures to contain the spread of the coronavirus.
Rennes also had a new coach on the bench as Bruno Genesio led the Brittany side for the first time since replacing Julien Stephan, who resigned earlier this month.