Ivory Coast's Gervinho bundled the ball home on 38 minutes after Ligue 1 top scorer Moussa Sow's effort was palmed on to the post.
The goal summed up a scrappy affair on a heavy pitch but the hosts, held at Auxerre last weekend, deservedly doubled their lead in stoppage time when Tulio De Melo scored on a breakaway at their small stadium.
Last term's fourth-placed side continue to confound those waiting for the bubble to burst for a modest team eyeing a first title since 1954.
Rennes, who lost to second-tier Stade de Reims in the French Cup last 16 earlier this month, broke the deadlock after 52 minutes thanks to Colombian striker Victor Montano's header and Togo's Razak Boukari netted a penalty soon after.
"It's a great satisfaction," said Rennes coach Frederic Antonetti, who told some of his players they were not good enough after the Reims loss.
"I've always said that there were five teams who have greater room to manoeuvre than us. Our aim is to be there if one of them doesn't make it."
One of the "big five", Paris Saint-Germain, were second going into the weekend games but drew 0-0 at home to Racing Lens on Saturday having lost 1-0 at Rennes last week.
Champions Olympique Marseille are third after Saturday's 2-1 success at Sochaux with PSG fourth on exactly the same record as Olympique Lyon who triumphed 4-1 at Saint Etienne in the weekend's big derby.
