The second half went largely the way of the first, with St Etienne creating the better chances but failing to capitalise.
Auxerre dominated for long periods without taking their chances and were made to pay for their profligacy as Claude Puel's side eased to what ended up being a comfortable win.
Auxerre made the early running with Devlin NDinga going through one on one with Hugo Lloris before losing his duel with the goalkeeper in the sixth minute. Lyon were looking out of sorts and shortly before the half-hour mark Roy Contout forced another save from the busy Lloris.
However, the home fans were stunned in the 31st minute when Boumsong forced the ball over the line from Cesar Delgado's cross after a partially-cleared corner. A minute into first-half stoppage-time Makoun doubled Lyon's lead, side-footing home past Olivier Sorin after good work from Anthony Mounier.
The game was over in the 65th minute when Lyon scored against the run of play once again. Pjanic found space in the area and, when Delgado's right-wing cross arrived, he was on hand to sidefoot home.