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.
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.
Govou's powerful shot hit the bar and bounced down with referee Alain Duhamel ruling the ball had crossed the line.
Kallstrom sealed Lyon's victory with a low 20-metre drive after 78 minutes.
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.
