"It's a success that has less to do with tactics than with emotional energy," Sampaoli said after becoming the first Marseille coach to win his first two league games since Elie Baup in August 2012.
"It's a victory won with energy, with will.
"It allows us to work with more serenity. We saw the unity of the group, the joy of winning. Now we have to start improving our game."
Arkadiusz Milik combined superbly with Dimitri Payet to score the opener at Stade Velodrome just before half-time, but Lilian Brassier's header brought Brest level with 20 minutes to play.
Thauvin swept home first time from Luis Henrique's pass to restore Marseille's lead on 88 minutes and Cuisance, who grabbed his first goal for the club with a late winner midweek against Rennes, came off the bench to add a third in stoppage-time.
"Thauvin's goal was important," Sampaoli said. "He came up to me to wish me a happy birthday."
Marseille climbed up a place to fifth, which offers qualification to the new Europa Conference League competition next season.
"A coach's struggle is to install an idea," Sampaoli said. "There will be different results and that's when we'll see the level of the team and if it can unite around a common project."
Payet said Sampaoli's approach had changed things.
"The coach wants us to attack, that brings this kind of match and three goals," the midfielder said.
League leader Lille is unbeaten in 10 games but on Monday's (AEDT) faces Monaco, which is fourth and had gone 12 matches unbeaten before losing at Strasbourg last time out.
Defending champion Paris Saint-Germain hosts struggling Nantes, with Neymar having come back from injury to train but not certain to start.
Lyon needed a stoppage-time equaliser from Zimbabwe international Tino Kadewere to salvage a 1-1 draw at Reims on Saturday (AEDT).