South African World Cup winner Dannie Rossouw, who has been added to the Toulon squad for the Heineken Cup quarter-finals, made his debut for the French leaders, while Gethin Jenkins, the man who led Wales to their successful RBS 6 Nations title last weekend against England, also got a rare start.
But Toulon rested outside half Jonny Wilkinson and paid the price. They also gave Australian midfield ace Matt Giteau a blow, were also without the injured Frederic Michalak behind the scrum and didn't have the power of Mathieu Bastareaud in the centre.
Utility back Benjamin Lapeyre was handed the pivotal No 10 jersey in Wilkinson's absence and had a miserable afternoon. By his own admission he "missed a try and some other opportunities" on his first outing in the position in three years.
Bayonne led 20-11 at the break and had tries from Scott Spedding, Marvin O'Connor and Sam Gerber at the heart of their victory. There was at least a losing bonus point to console Toulon director of rugby Bernard Laporte thanks largely to tries from Jean-Charles Orioli, Joe van Niekerk and Sebastien Tillous-Borde.
Toulon travel to Paris to face Stade Francais in their final game before hosting the Tigers in their first home Heineken Cup quarter-final on Sunday, 7 April. The Tigers, meanwhile, will meet arch-rivals Northampton Saints in their final fixture following their 12-6 win at Exeter Chiefs this weekend.