Early goals from strike duo Karim Benzema and Fred put the visitors in control and Kim Kallstrom added a third six minutes after the interval.
Frederic Thomas pulled one back for Auxerre 12 minutes from time but it was not enough to affect the outcome as Les Gones finished four points clear of Bordeaux, who were held to a 2-2 draw at Lens.
That result meant Jean-Pierre Papin's Lens were relegated to Ligue 2 following Toulouse's 2-1 home victory over Valenciennes.
Lens twice went behind to goals from Fernando Cavenaghi and substitute David Bellion after 66 and 80 minutes respectively. They battled back within four minutes of going behind each time - through Olivier Monterrubio and Toifilou Maoulida - but it was not enough.
Toulouse enjoyed the perfect start to their match when Jeremy Mathieu put them ahead after just five minutes.
VA levelled through Johan Audel six minutes before the break but Pantxi Sirieix's winner 15 minutes from time ensured Toulouse will be playing top-flight football next season.
Paris St Germain also ensured their safety with a 2-1 victory at Sochaux, Amara Diane notching a goal either side of Guiranne N'daw's equaliser.
The other major battle to be decided on Saturday was the one for third spot and it was won by Marseille, thanks to their 4-3 victory over relegated Strasbourg and Nancy's 3-2 defeat at home to Rennes.
Elsewhere St Etienne finished fifth after thumping Monace 4-0, relegated Metz finished the season with a 4-3 win over Le Mans, Nice claimed a 3-1 win over Caen and Lille earned a 1-1 draw at Lorient.