"Crossing the finish line in first was amazing. I would not be able to claim the jersey without the work of this team," said Thomas.
"They were amazing all day and we knew we had multiple cards to play – it just happened to come down to a sprint so I knew it would be my job to seal the deal.
"I was confident I could win the race if it came down to a bunch sprint, I really wanted to bring it home for the team.
"I wouldn't call myself a pure sprinter, but I did the absolute best I could to win the Tour.
"We've raced really well together all week and it's been amazing to see the teamwork and confidence that has come out of this team.”
Elise Chabbey, her Bigla teammate, crossed just behind in second but that wasn't enough to move her up enough in the GC standings as Stage 2 winner Alison Jackson finished second.
Meanwhile Stine Borgli repeated her third-placed second-stage finish in Edinburgh to finish third overall in Scotland.
With 5km left to ride it looked like Cecilie Uttrup Ludwig (Team Bigla) was set to win the race with a ten-second lead, although she was caught on the final climb.
The Dane still took home the EventScotland Queen of the Mountains Jersey for her team after an impressive five victories in the competition over the course of the weekend.
Stage 3 was a resounding success for Team Bigla with 22-year-old Belgian rider Nikola Noskova taking the Deloitte Best Young Rider Jersey, while Anna Shackley secured the Best Scottish Rider Jersey in the capital.
"I am really pleased to win the jersey, especially because it was my first UCI race," said Shackley. "I was quite surprised, but I am happy with my performance overall.
"The heavy rain made the surface a lot slippier when we were coming down the hill near Arthur's Seat.
"It was quite scary at points, but it definitely made the race more interesting.
"Having the crowds at the finish line was so nice, some of them know me by name and it was so nice to hear them cheer."