Lyon's France winger Sidney Govou struck from 25 metres after only seven minutes and Sweden midfielder Kim Kallstrom grabbed their second goal with 12 minutes left as Lyon moved on to 20 points from eight matches.
Bordeaux are a point back after losing 3-1 at lowly St Etienne earlier on Saturday. It was their first defeat in 23 matches in all competitions.
Augusto Fernandez and Ilan scored in the first half as Bordeaux, without France playmaker Yoann Gourcuff through injury, struggled to find their rhythm.
Bordeaux's Brazilian forward Jussie converted a 69th-minute penalty to reduce the arrears but substitute Dimitri Payet added a third goal for the home side in stoppage time.
"We are very disappointed but it happens. We knew we would not be unbeaten all season," Bordeaux goalkeeper Cedric Carasso told French TV channel Foot Plus.
TAKING COMMAND
Lyon did not waste their chance to secure first place as they swiftly took command at the Felix Bollaert stadium.
Govou's powerful shot hit the bar and bounced down with referee Alain Duhamel ruling the ball had crossed the line.
Lens defender Yohan Demont missed a penalty in the 36th minute after Anthony Reveillere handled in the box.
Kallstrom sealed Lyon's victory with a low 20-metre drive after 78 minutes.
Lens, with three defeats in their last four league games, slipped to 16th, only one point above the relegation zone.
Promoted Montpellier moved up to third as they snatched a 3-2 win at bottom club Grenoble, who have lost their first eight league games in the worst start to a French top flight season.
Paris St Germain's Benin midfielder Stephane Sessegnon salvaged a 1-1 home draw with Nancy but PSG, who are fifth, have now failed to win in their last four league games.
Stade Rennes, who had Carlos Bocanegra sent off after 16 minutes, lost 1-0 at home to AJ Auxerre and slipped to sixth.
Olympique Marseille, without injured Brazilian forward Brandao, take on neighbours Monaco on Sunday.
