The 29-year-old, who has scored two goals for the Latics so far this season, has put pen to paper on a two-and-a-half-year contract.
"We're delighted that Shaun has committed his future to the club," manager Roberto Martinez told Wigan's official website.
"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."
Maloney moved to the DW Stadium from Celtic in 2011.