Rennes goalkeeper Benoit Costil diverted Alexandre Lacazette’s penalty onto the post, although Lyon eventually opened the scoring through Maxwel Cornet on 52 minutes.
But substitute Mubele powered in from the edge of the area nine minutes from time, and Rennes nearly snatched all three points as Sanjin Prcic fired into the side netting after following up his initial strike.
“Taking everything into account, we should have picked up three points. So yes, this draw is like a defeat,” groaned Lyon coach Bruno Genesio.
“It’s a match that sums up our season well. With what we showed today, we don’t deserve to be fighting for the top three.”
Lyon remain fourth and a distant 16 points behind Nice in the final Champions League spot with just eight games left to play.
Benjamin Moukandjo netted his 10th goal of the season as Lorient won 1-0 at home to Caen to climb off the bottom, while Prejuce Nakoulma netted twice as Nantes defeated Angers 2-1.
Andy Delort’s first-half strike earned Toulouse a 1-0 victory at Montpellier as the visitors were forced to wear an all-white uniform provided by their opponents to avoid a kit clash.