Thomas crashed dramatically in the final hundred metres as he attempted to sprint for the win against Michael Woods on Stage 4, but put that disappointment behind him as he finished third on the final stage - a 16.2 kilometre time trial in Fribourg - to win the race overall.
Michael Woods (Israel Start-Up Nation) was in the race lead heading into the time trial, but his 28th placed finish, 54 seconds behind Thomas saw the Canadian slip to fifth overall.
Remi Cavagna (Deceuninck-QuickStep) won the stage with a time of 21 minutes and 54 seconds over the hilly course in wet and windy conditions, beating out Stefan Bissegger (EF-Nippo) by six seconds.
Australian overall contender Richie Porte moved up as well on the time trial jumping up from fifth to second overall with his fourth-placed finish on the time trial, but it was Thomas who carried the day with the overall win after putting aside the misfortune of the previous stage.
“I’m very happy, especially after the little mishap yesterday - which wasn’t ideal," said Thomas. "That definitely made it more of a challenge today but I felt good.
“To be honest it kind of reminded me of when I won the Tour back in Espelette, it was kind of like this, the last descent on the radio they were telling me to ‘take it easy’ and just ‘don’t do anything stupid, don’t crash on the corners’ and then obviously you overthink it a bit then. I’m really happy to finish it off and it’s been a great week with the team."
Thomas was still the favourite to take the overall, starting the final stage just 11 seconds behind weaker time triallist Woods, but with questions lingering over the effect of the crash on Thomas' condition there was still some intrigue in the final result.
“Today was all about trying to take the jersey and get around safe," said Thomas. "Obviously, I would have loved to have gone for the stage, but that last descent it was a bit wet, so best to just take it steady and finish the stage rather than risk it all."
The 2018 Tour de France overall was the Welshman most recent victory in what has been a few seasons that have seen Thomas set back by injury.
“As we all know bike racing is about winning but it’s not like I haven’t performed since I won the Tour," said Thomas. "I was second in the Tour the next year, second in Tirreno, third in Catalunya. I’ve been up there but it’s nice to finally get the win.”
“At the start of the year, I said my goal was the Tour and every race was a build up to it and didn’t really put any pressure on myself to perform early, but I seem to have come into some good shape pretty soon. I’ve had a lot of good races building up, obviously Catalunya was really good for the team, I was third there behind two teammates, which was amazing to be a part of.
"I knew I was going well and myself and Richie wanted to come here and make sure one of us won the race. First and second - we can’t complain!"
There were two other Australians that finished in the top ten, with Ben O'Connor (AG2R-Citroen) slipping a few spots from third to sixth overall, while Lucas Hamilton (Team BikeExchange) remained in eighth overall after a solid time trial performance.
Australian time trial specialist Rohan Dennis (INEOS Grenadiers) was ninth on the stage and finished 17th overall after leading the race for the opening three stages.
