After finishing safely in the bunch sprint of the fifth and final stage in Germany, the Welshman - who entered the last day with a commanding lead in the general classification - added the overall title to stage wins for team-mates Edvald Boasson Hagen and Bradley Wiggins.
Giacomo Nizzolo of Leopard Trek won the stage in a time of three hours and 40 minutes dead after a 162.1 ride from Friedberg to Moosburg.
HTC-Highroad’s John Degenkolb was second, ahead of Boasson Hagen, who thus won the sprinters jersey.
Nicki Sorensen of Saxo Bank and HTC’s Michael Albasini rounded out the podium for the GC.
"It’s great, I didn’t really expect it coming into the race as we had Eddy and Brad and Christian (Knees) as well - we thought all four of us were capable of winning it and to be in that position is fantastic," Thomas said.
"It was a great end to the week - we’ve been on the podium every day as well so it’s a great race for us.
"We’ve all worked really well together this week. Even without radios, we’ve known exactly what we’ve had to do and we’ve all communicated really well.
"I think it shows that after a full year together we are really starting to gel as a unit and as a team. It’s really paid off this week."
Stage five podium:
1. Giacomo Nizzolo (Leopard Trek) - 3:40:00
2. John Degenkolb (HTC-Highroad)
3. Edvald Boasson Hagen (Team Sky)
1. Geraint Thomas (Team Sky) - 19:09:36
2. Nicki Sorensen (Saxo Bank) - 17s
3. Michael Albasini (HTC-Highroad) - 19s