Props Adam Jones and Gethin Jenkins are preferred to Chris Horsman and Duncan Jones in the front row.
Thomas is joined on the bench by fly-half Stephen Jones, who has recovered from a serious hip flexor injury but has not played any rugby since the first week of May.
Peel, the Lions scrum-half in 2005, was named in a six-strong senior leadership team when the World Cup squad was announced and he becomes the 124th player to captain Wales.
Head coach Gareth Jenkins explained: "Gareth (Thomas) put in three royal performances for us during August, but this is the first time Sonny Parker has been available to us to start a game so we are giving him a chance in the centre.
"We have been saying for some time that we will use more than one captain during this tournament and Dwayne was always one of three players who will potentially captain the side at this World Cup alongside Gareth and Stephen.
"He is one of our identified leaders, a core member of the squad and the very definition of a professional rugby player.
"He will cope admirably with the responsibility of captaining his country. He follows in the footsteps of some great players and we know he will do justice to the honour that has been bestowed upon him."
Jones was rested for Wales' summer tour to Australia and then missed the three August Tests after injuring his hip flexor in training at the end of July.