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The French striker opened the scoring on the half-hour mark when he found the bottom corner of the net to fire Les Pitchouns ahead.
Ben Yedder added his second before the interval from the spot, before Anthony le Tallec pulled a goal back for the visitors from close range.
Toulouse made sure of the points through Ben Yedder once more, with the 23-year-old completing his hat-trick with a left-footed strike after being picked out by Dusan Veskovac.
Toulouse finish the season in ninth place, while Valenciennes will be taking part in the second division of French football next season.