Forward Karim Benzema opened the scoring with a diving header from Florent Malouda's cross after 17 minutes and captain Thierry Henry doubled the advantage from the penalty spot after defender Rod Fanni was blocked in the box.
Striker Marc Janko reduced the deficit for the visitors early in the second half before substitute striker Andre-Pierre Gignac sealed the win with a superb angled shot after 66 minutes.
Nothing was at stake with France certain to finish second behind Serbia to go into a two-legged playoff on November 14 and 18 and Austria already eliminated.
France's playoff berth was secured on Saturday when they thrashed Faroe Islands 5-0 in Guingamp while Wednesday's win earned a measure of revenge for the 3-1 defeat to Austria in their opening qualifier that eventually proved so costly.
The former world and European champions looked sluggish at first and survived a scare when Hugo Lloris did well to save a powerful shot from 20 metres by Stefan Maierhofer.
Gradually, however, the home side moved on top of opponents certain to finish third in the group whatever the outcome and the two goals midway through the first half put them in control.
Henry, holding his thigh, limped off early in the second half, with his replacement Gignac making an instant impact.
There was a moment of confusion in the closing stages when two spectators invaded the pitch and had to be removed by security.
