Morocco striker Chamakh headed home with four minutes left as champions Bordeaux extended their lead to four points over Montpellier, who earlier cemented second place with a 1-0 victory at Toulouse with a 10th-minute Souleymane Camara strike.
Bordeaux have 34 points from 16 games before travelling on Wednesday to promoted Montpellier, who have 30 points and one game in hand.
"We did not let them gain confidence in the first half," Bordeaux coach Laurent Blanc told French TV channel Canal Plus. "We could have settled for a draw but we play games to win them."
Lyon defender Cris, angry with team mates, said: "We lack character on the pitch. If you want to play at Lyon, you have to show something else."
Bordeaux centre back Lamine Sane, deputising for the injured Michael Ciani, did an excellent job keeping Lisandro Lopez at bay in his first top flight game.
Bordeaux keeper Cedric Carrasso did not have much work until the 76th minute when he parried away a sudden, powerful 30-metre drive by midfielder Maxime Gonalons.
Both teams looked resigned to a dull draw when Chamakh surged at the far post to net the winner from a Yoann Gourcuff cross.
Lyon, who have not won in their past five league games, slipped to ninth on 26 points.
Brazilian forward Tulio de Melo struck twice to help Lille thrash Monaco 4-0 away. The northern side clinched their sixth win from their last seven league games to move up to third on 28 points from 17 matches.
Elsewhere, Peguy Luyindula, Stephane Sessegnon and Mevlut Erding found the back of the net before the break as Paris St Germain beat strugglers St Etienne 3-0 at home.
PSG gained one spot up to 10th on 25 points, while St Etienne remained 17th, three points above the relegation zone.
Sochaux beat Grenoble 1-0 at home, handing the bottom side their 12th defeat of the season.
