The 29-year-old Scotland international, signed for £1million from Celtic early last season, is now contracted to the Latics until 2015.
Roberto Martinez said: "We're delighted that Shaun has committed his future to the club."
Maloney has become a key figure at Wigan having started all but two of the strugglers' 22 Premier League games this season and scored twice.
After three years at Celtic, he arrived at Wigan in August 2011 hoping to re-establish himself in the English top flight after a previous spell at Aston Villa.
He has now made 33 league appearances in total for Martinez's side and played a key role in their dramatic escape from relegation last year.
Martinez said: "From the first day he arrived his professionalism and determination to succeed has been outstanding and an example for the younger members of the group to follow.
"Shaun is one of the most technically-gifted British players that you will find, but on top of his style and footballing flair his work-rate and purpose in his performances make him a key member of our future at Wigan Athletic.
"I'm sure the fans are looking forward to watching him continue to enjoy his football at Latics for a long time."
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