A second-half goal from Senegalese captain Abdou Khader Mangane and a penalty from Sylvain Marveaux completed the victory and took Rennes to the top for the first time since 1970, with 18 points after an unbeaten run of eight games.
Toulouse had dominated the first 45 minutes but could not convert possession into chances. They pulled one goal back through Moussa Sissoko in the 88th minute and fell to fourth spot on 14 points.
Earlier, Senegalese striker Moussa Sow scored twice for Lille to help the club move up to third place with a 3-1 home win over Montpellier.
Sow, who signed on a free transfer from Rennes in June, could have had a hat-trick but hit the bar as Lille ran rampant in the opening half when France international Yohan Cabaye also smashed a shot against the bar.
"We had a good game, especially in the first half and linked up well," Lille coach Ruudi Garcia said. "We showed we were able to raise our game."
PSG HELD
Montpellier, last year's surprise package, had levelled the score three minutes after Sow's 19th-minute opener through a penalty taken by Olivier Giroud, his fourth goal of the campaign.
Ivory Coast striker Gervinho wrapped up the three points with the northerners' third goal 10 minutes from time.
Lille, also unbeaten this season, are third on 14 points ahead of Toulouse and newly-promoted Brest on goal difference.
Paris Saint-Germain were held to a goalless draw by a dogged Nice side, leaving them in seventh place with 12 points.
PSG, who had a second win in the Europa League on Thursday, were unable to continue their good early-season form as Nice's Colombian keeper David Ospina pulled off a string of saves to earn his side a point in the capital.
"We need to work harder to become one of these big clubs that can turn tight games into 1-0 wins," PSG forward Guillaume Hoarau said.
Saint Etienne are second after Saturday's 1-1 draw with Marseille.
