The frontman - renowned for his wild ways and partying lifestyle - tied the knot in a surprise ceremony surrounded by family and friends, held directly after the christening of the couple's ten month old daughter, Lulu, at St Charles RC Church in Manchester.
The wedding guests hadn't been told ahead of the event, and believed they were only attending the christening.
Shaun's manager, Warren Askew, said: "Congratulations to Shaun and Joanne on their wedding. It was a surprise to everyone after the baptism of Lulu, but was a really lovely day."
47-year-old Shaun - formerly renowned for his 'bowl' haircut and penchant for sportswear - looked dapper for the day in a blue suit, tie and parted hair, with a blue tinted pair of spectacles.
Shaun's post Happy Mondays band, Black Grape will appear for a special one off show on April 1 in London, and the singer has admitted he will have to use an autocue machine to remember the words.
He said: "I've got an autocue so I don't sing the wrong lyrics at the wrong gigs. "It's not cheating as everyone uses one. How does someone who has written hundreds of songs remember them all?
"If you'd written The Godfather you wouldn't be able to read it to somebody without the book."