Lyon stretched their unbeaten run to eight games but remained in third spot with 50 points from 27 matches, two points behind leaders Girondins Bordeaux and Montpellier who drew on Sunday.
Lille are now on 48 points after drawing 1-1 at St Etienne.
Emmanuel Riviere put St Etienne in front before Stephane Dumont equalised in the 21st minute.
Lyon paid the price after resting strikers Lisandro Lopez and Cesar Delgado and midfielders Jeremy Toulalan and Miralem Pjanic ahead of Wednesday's Champions League last-16 second leg at Real Madrid.
The visitors were reduced to long-range efforts and rarely troubled goalkeeper Jean-Francois Bedenik.
Boulogne ended the game with 10 men after Yoann Lachor received a second yellow card in stoppage time.
"We met a rather good team but I think our attack lacked efficiency," Lyon midfielder Kim Kallstrom told reporters.
Elsewhere, Racing Lens and Paris Saint-Germain shared a 1-1 draw.
Sebastien Roudet gave Lens the lead in the 67th minute but Stephane Sessegnon levelled four minutes into added time.
Sixth-placed AJ Auxerre, Stade Rennes and Sochaux recorded 1-0 home wins over Valenciennes, Monaco and Toulouse respectively while Nancy triumphed 3-2 at Nice.
