Thomas, who missed last weekend's victory over the Pacific Islands, regains the captaincy after Llanelli Scarlets fly-half Stephen Jones failed to shake off a knee injury.
Jenkins' selection to face World Cup group opponents Canada features only three changes from the side that drew 29-29 with Australia on the opening weekend of the autumn series.
Thomas moves to full-back in place of Kevin Morgan, allowing winger Mark Jones keeps his place on the wing after an impressive try-scoring performance against the islanders.
Man of the moment James Hook returns to fly-half, where he produced a star turn against the Wallabies, with Gavin Henson and Tom Shanklin paired together in the centres.
Jenkins has named the same pack that started against Australia, with Matthew Rees, Gethin Jenkins and Adam Jones in the front row.
Ian Evans and Ian Gough form the second row, Ryan Jones starts at number eight with the pack flanked by Martyn Williams and Jonathan Thomas.
Jenkins explained: "Alfie (Gareth Thomas) needs to play and with Stephen injured he is the ideal person to come in and captain the side as we try to lay down a World Cup marker with Canada.
"Mark Jones retains his place on the wing and has another opportunity to show what he can do after having an impressive performance against the Pacific Islanders.
"Ceri Sweeney also went well at fly-half last week, but we felt James Hook would benefit from another 80 minutes or so at international level, plus we get another chance to assess how he fits into the set-up."
Jenkins had next weekend's clash with New Zealand in mind when making his selection.
He has included the likes of Sonny Parker and Sweeney, who both shone against the islanders, on the bench.
"We have selected a side to beat Canada and there are other players in the squad who impressed against the South Sea Islanders who may yet come into the equation this series as the shadow of the New Zealand match looms over us," said Jenkins.
"We had a healthy debate this week about selection and are another step closer to finding the 22 players who will represent Wales against All Blacks."