The former La's frontman came out onstage to perform his band's album track 'Son Of A Gun', NME reports.
He also returned during the encore at the Birmingham Academy to perform his top 20 hit 'There She Goes'.
Babyshambles manager Adrian Hunter said: "Lee and Peter met via John and Gary Bandit. There was an impromptu jam in the dressing room last night pre-gig, and 'Son Of A Gun' was included in the set.
"'There She Goes' was only added before the encore with no rehearsal at all, although everyone obviously knew the song."
He added that "you never know" if Mavers could return for other dates on the tour to play with Doherty and his backing band, made up of Stephen Street, Graham Coxon, Drew McConnell and Adam Ficek.
Doherty covered a number of songs by The La's on The Libertines's Babyshambles Sessions bootleg discs in 2003, including 'Son Of A Gun'.