Tries from Scott Spedding, Marvin O'Connor and Sam Gerber put Bayonne in control inside the opening 50 minutes, and though Toulon hit back with scores from Joe van Niekerk and Sebastien Tillous-Borde, Bayonne hung on to claim a big scalp.
Toulon retained their place at the top of the table, however, as Biarritz also earned a big win as they left it late to beat second-placed Clermont 32-28.
Benoit Baby's try seven minutes from time - and conversion by Dmitri Yachvili - was enough to see Biarritz home after Clermont had appeared to pinch it with two tries in three minutes in the final quarter of an hour.
Bordeaux-Bègles smashes Mont-de-Marsan 40-7, Grenoble went down 16-9 at home against Montpellier, Castres cruised past Agen 20-9, and Racing Metro withstood a late onslaught at home against Perpignan to scrape home 23-19.
- Sports & Recreation