The Brazilian forward, who got the extra-time winner in last year's final for Marseille, found the net in the 18th minute from a Pierre-Emerick Aubameyang cross.
Brandao now has four straight League Cup winners' medals to his name, having won the previous three finals with Marseille.
St Etienne, who dominated the match in a friendly atmosphere at the Stade de France, picked up their first silverware since the last of their record 10 French league crowns in 1981. The victory secured a place in next season's Europa League play-offs.
"The whole squad made it. I'm very happy for the team, for all the fans. It was very important for St Etienne," Brandao told French television channel France 2.
"When I sign for a team, I want to win trophies. I told them we had to seek a trophy when I joined," added the Brazilian, who was named man of the match.
St Etienne coach Christophe Galtier paid tribute to his match-winner. "It's obviously a collective achievement. But he, he's a Cup winner, he's a leader," he said.
Rennes, who lost the French Cup final to second-tier Guingamp in 2009, have still not won a trophy for 42 years.
Rennes coach Frederic Antonetti told a news conference: "I would like to congratulate the boys because they fought as hard as they could regarding our weapons of the moment."
"I can't blame them because they gave everything they had."
The two sides both started an entertaining game well, each creating a clear-cut chance in the first two minutes.
Moments later, a volley by St Etienne's Francois Clerc from a Yohan Mollo corner went narrowly wide.
The green half of the packed crowd did not have to wait long to roar a goal as Brandao tapped home to put St Etienne ahead.
Seven minutes later, Rennes' goalkeeper Benoit Costil prevented the Brazilian from doubling the lead by palming away his powerful header at the far post.
Les Verts controlled a one-sided first half and went close to a second goal soon after the break but Renaud Cohade somehow missed the target following Mollo's run down the left wing.
Rennes, who had lost striker Erding to injury midway through the first period, tried to stage a fight-back but did not really manage to threaten Ruffier.
Rennes winger Jonathan Pitroipa failed to shine and his main contribution was a clearance on his own goal line following a Clerc header in the 53rd minute.
Ruffier, who had enjoyed a fairly quiet night after his first-minute save, made a superb stop to deny Sadio Diallo with four minutes to go and preserve St Etienne's slender lead to ensure they could celebrate a long-awaited triumph.