Cameroon striker Njie netted his second goal in as many games 12 minutes from time to put OL on 51 points from 25 games two ahead of Olympique de Marseille and Paris St German who were also held to draws at the weekend.
Lorient are 16th on 28 points, two points above the danger zone after Njie cancelled out Jordan Ayew's 50th minute goal.
Lyon were far from their best in a dull first half during which they failed to create a single chance.
Lorient made them pay when Ghana forward Ayew headed home from Benjamin Jeannot's cross from the right.
That spurred Lyon into action but Benjamin Lecomte denied Nabil Fekir from close range with a superb save in the 55th.
Njie equalised in the 78th minute after second-half substitute Yoann Gourcuff set up Henri Bedimo on the left flank.
The Cameroon defender's cross was met by Njie, who beat Lecomte with a low shot that was deflected off a defender.
Lyon continued to push forward and Christophe Jallet's volley from just outside the box was tipped away by Lecomte in the 84th.
PSG were held to a 2-2 draw by lowly visitors Caen on Saturday as injuries meant they finished the game with nine men after Marseille also drew 2-2 at home to Stade de Reims on Friday.
(Reporting by Julien Pretot; Editing by Ken Ferris)
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