Tries from Charlie Davies, Joe Launchbury and Tom Varndell maintained a 100 percent record and secured their qualification as Pool Four winners.
Outside-half Andy Goode and Bayonne wing Martin Bustos Moyano exchanged two penalties each early on before Goode edged Wasps back in front with his third.
Davies scored Wasps' first try just before half-time but Goode missed the conversion and then two penalties within 10 minutes of the second half beginning.
It looked costly as Bayonne got their first try through flanker Mark Chisholm, with Bustos Moyano adding the conversion.
Goode missed a third penalty before Launchbury scored Wasps' second try, with replacement Joe Carlisle slotting the conversion.
Varndell secured the win nine minutes from the end after excellent work by replacement scrum-half Joe Simpson.