Roberto Martinez had sought to sign the Bolton goalkeeper after he proved valuable during a loan spell last season, when he was named the club’s player of the year.
The Latics had previously made three unsuccessful bids for the player, refusing to meet the asking price of £4m.
“We could easily have kept him but I have to be fair to Ali,” said Bolton manager Owen Coyle. “He did well at Wigan last year and they have tried to secure his services.”
The Omani international joined Wigan in January 2006, since which he has made 18 appearances for the club due to the prominence of Jussi Jaaskelainen.
Aston Villa had also had their eye on the 29-year-old as a replacement for Brad Friedel.