The Oman goalkeeper enjoyed an excellent year on loan at the DW Stadium last term but Latics manager Roberto Martinez had taken his time trying to sort out a permanent deal.
Up for the battle: Ali Al Habsi is on the brink of agreeing a ?4m switch to Wigan
However, a transfer in the region of ?4million has now been concluded.
Martinez said: 'We are delighted to announce the best possible news for Wigan Athletic in securing Ali permanently.
'During his loan at our football club last season, Ali brought a great degree of professionalism in his daily work and put in many outstanding performances in the Premier League.
'Goalkeeping is a very specific position and we are very pleased that we are going to be very strong in this department going into the new season.
'Being voted player of the season reflects the huge impression that Ali had on the pitch but also the feeling of the supporters towards him.
'After making it really clear that he wanted to play for Wigan Athletic moving forwards we've done everything possible to make this happen.
Say my name: The Oman stopper became a fans' favourite at the DW Stadium last term
Staying put. for now: Cahill reported for Bolton's pre-season training
'The chairman [Dave Whelan] and everyone at the football club are delighted that Ali will be staying andI'm sure every single Latics fan will feel extremely proud and be able to enjoy a great day after hearing this news.'
Al Habsi joined Bolton in 2006 but made just 10 league appearances for the Trotters.
He made his Wigan debut in the 1-0 win at Tottenham last August and kept eight Barclays Premier League clean sheets in all - including a vital one in the final game of the season as the Latics avoided relegation thanks to a 1-0 win at Stoke.
He said: 'I am very happy. I want to thank everyone at Bolton for helping me get established in this country but I need to be playing first-team football, and hopefully, if I can stay fit and keep doing my best, I will get the chance again at Wigan.
'I think the gaffer is building a really exciting young team here and I am thrilled that I can be a part of that again.
'I am so grateful that the gaffer gave me the chance to prove what I can do and now I want to repay him, and the Wigan fans, for making me so welcome last season.'
Meanwhile, England defender Gary Cahill returned to Bolton training despite huge speculation over his future, with Tottenham and Arsenal amongst those believed to be interested.
'Gary has been the subject of speculation every day, probably to the point he is frustrated by it,' said boss Owen Coyle.
'I have been very open. Some of the elite clubs in this country have noted their interest.
'But there has been nothing concrete. Until that changes, Gary is a Bolton player.'
Coyle has already moved to strengthen his squad by securing former Swansea midfielder Darren Pratley on a four-year contract.
'Twelve months ago, Swansea turned down bids in the region of ?2million-plus, so it is a good bit of business,' said Coyle.
'He is a very good player. That is the important thing. He has a point to prove.
'He wants to show he is a bona fide Premier League player and I am excited to have him.'
Coyle is on the hunt for at least one more striker given Johan Elmander and Daniel Sturridge have both departed this summer.
Shaun Wright-Phillips and Robbie Keane are both believed to be on Bolton's radar, although Coyle claims there is nothing to report. "We have been trying to bring one or two in, and we will continue to do that," he said.
Villa manager McLeish sets sights on ?4m Bolton stopper Ali Al Habsi Bolton reserve stopper Al Habsi set to complete ?4m switch to Wigan Explore more:People: Johan Elmander, Robbie Keane, Shaun Wright-Phillips, Gary Cahill, Owen Coyle, Daniel Sturridge, Roberto Martinez Places: Oman, United Kingdom