Stelling revealed in April that he will be leaving the show after over 25 years in charge.
The legendary presenter was given a standing ovation by colleagues Paul Merson, Clinton Morrison, Kris Boyd and Matt Dawson on what was an emotional final appearance.
He also revealed that he received a surprise call from music icon Elton John to thank him for his service.
With the new campaign just around the corner, Sky have announced that Thomas will be the new presenter of the hit show.
He has over 20 years of experience in broadcasting and has previously spent more than a decade at Sky Sports.
READ MORE ON TRANSFERS
Rice to Arsenal means England's three most expensive stars all could've played for Ireland
Newcastle hope to sell Allan Saint-Maximin to fund move for West Ham target Barnes
The 50-year-old has fronted coverage of both the Premier League and EFL in the past, and presented Sky Sports News.
He said: "When I left Sky in 2018 for very personal reasons; it was always said the door would be open if I ever wanted to return. I never expected that Gillette Soccer Saturday would be the door that would open.
"Being asked to present this iconic show and follow in the footsteps of Jeff Stelling, an absolute giant of sports broadcasting, is a massive honour and one I simply cannot wait to get started on."
Thomas will not be the only new arrival on Gillette Soccer Saturday as former referee Mike Dean will also join the team.
Most read in Football
West Ham in talks with Rice replacement, Onana set for Man United, Lukaku latest
Harry Maguire announces he is no longer Man United captain in heartfelt post
Onana to complete Man United transfer in next 24 hours and will join in time for US tour
Harry Maguire urged to consider West Ham transfer as Man United exit rumours persist
He is set to offer in-depth analysis and insight on the big decisions made next season after stepping down from his Premier League VAR role and 27 years experience as a referee.
Soccer Saturday will also be broadcast from a new studio with Merson, Morrison, Boyd, Dawson, Sue Smith and Tim Sherwood also part of the team.
For mid-week matches, Julien Warren will continue his role as presenter.
Soccer Saturday first appeared on TV screens in 1992 and is close to making its return for the new English football season.