The Oman international spent last season on loan at the DW Stadium and was keen to return but the deal was held up because the two clubs could not come to an agreement on the fee.
However, the Latics are believed to have met Wanderers' £4million valuation and Al Habsi, Wigan's player of the season, was able to make his move permanent.
Al Habsi was Wigan's player of the season last term and he revealed, after four years as the understudy to Jussi Jaaskelainen at Bolton, it was the first time he felt like a real professional footballer.
"To come from Bolton on a season loan and get player of the year was great - especially as it was the first time in my life I had played like a professional in terms of every week," said the 29-year-old.
"The thing with Bolton was Jussi Jaaskelainen was there but I showed myself 100% when Jussi was injured and I got my chance and so everyone knew what I had.
"In the end this is football. Every manager has his ideas and the most important thing was when I was there I gave 100%.
"But I want to say thanks to the gaffer (Wigan boss Roberto Martinez) for giving me the confidence to come to his club.
"It is like my club now having already been here for a season.
"At my age this is the time to play week after week and I think I have come to the right club.
"Now it is my job to show myself more than I showed last season."
Martinez made Al Habsi's signature his priority this summer and although there was a time when it seemed the deal was deadlocked because of a difference of opinion on the price, the Spaniard was confident it would go through.
However, he would have liked it to have been more straightforward, but at least he has secured the player before the squad start back for pre-season training later this week.
"I wouldn't say it was a predictable signing," said the Spaniard.
"When you know that something could happen that is often the hardest one to achieve but I am extremely pleased Ali was focused to come here and we have signed a player we wanted.
"When you are signing a good player it is never easy.
"Ali had a phenomenal season, winning the player of the year award, and to do that as a loan player says a lot about him.
"We signed him for the long term, someone who is a true ambassador for the club.
"He is the right age in terms of goalkeepers and I am extremely pleased.
"I know the fans will be delighted. We had to work really hard to get a player who it was well known had had a terrific season but I know has another level to go to."
Al Habsi is confident he can better his performances last season, when the club fought against relegation until their safety was secured on the last day of the season.
"I have to show more for the fans because the support they showed me last season was fantastic," added the goalkeeper.
"The way we finished last season, everyone was so happy. We have to improve and take it to the next level."