Maloney, who turns 30 next Thursday, has signed until the summer of 2015 by which time he will be 32.
The move has been taken following the impressive form of the former Celtic forward since his integration into the Latics first team last season.
Maloney has grown to be a firm fans' favourite at the DW Stadium and Roberto Martinez is delighted with the news.
Speaking to the club's official website, he said: “We’re delighted that Shaun has committed his future to the club. 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.