Truffert, 18, claimed the winner after assisting Steven Nzonzi's equaliser as Wissam Ben Yedder broke the deadlock in the first half.
Monaco coach Niko Kovac made four changes from Sunday's victory over Nantes with Ben Yedder captaining the side.
The Bretons' Serhou Guirassy kept his place up-front after scoring twice in last weekend's win at Nimes.
Ben Yedder opened the scoring after 28 minutes following a defensive shambles inside the Rennes box.
Sofiane Diop hit a half-volley after a Cesc Fabregas corner and Ben Yedder hit home following Steven Nzonzi's attempted clearance.
Nzoni made up for his earlier mistake with nine minutes to play.
Left-back Truffert broke down the flank and the former Blackburn and Roma midfielder headed the equaliser.
Ben Yedder was substituted with seven minutes left as the visitors looked to close out a point.
Truffert had other plans, scoring the winner less than 70 seconds into injury time with a shot from outside the box.
Newly-promoted Lens moved up to third with a 2-1 win over Bordeaxux.
Summer arrivals Ignatius Ganogo and Chelsea academy product Gael Kakuta were on the scoresheet before Samuel Kalu's consolation effort in injury time.