Thomas sealed overall victory in the prestigious race for the first time - becoming the fifth British victor in its history - after successfully defending his overall lead as second-placed compatriot Adam Yates (Mitchelton-Scott) won the final stage on St Gervais Mont Blanc.
Thomas suffered in the final kilometer of the grueling 136-kilometer trek featuring three punishing ascents and finished the stage in fifth place, 19 seconds back.
The 32-year-old Thomas, victor of Paris-Nice in 2016, is coming into form at just the right time with the Tour de France a month away.
Thomas added to ITV: "I always felt in control, I always felt pretty good, but I didn't want to get too carried away (on the final climb)".
It came on a 110 kilometres stage from Frontenex which is nearly a carbon copy of this year's Tour de France stage 11.
"Without the boys here I would not have won the Dauphine".
Yates said: "The Tour de France has been my main goal for the whole season".
Ireland's Dan Martin resisted a late challenge from Welsh all-rounder Geraint Thomas to clinch his first win in 16 months after a thrilling summit duel at the Criterium de Dauphine on Friday.
"I made a good recovery though and I'm in good shape, ready for the next training block ahead of the Tour".
Yates' victory was his second on the WorldTour this season, after also winning a stage at Tirreno-Adriatico, as he powered clear of Thomas and Romain Bardet (Ag2r-La Mondiale) in the final 200m.
"Each kilometre I was more confident and happier". Emanuel Buchmann (GER/BOR) 14, 5. Romain Bardet (FRA/ALM) 09, 4. Pierre Latour (FRA/ALM) 35, 10.
Thomas is next due to race in the National Road Race championships in Northumberland where he is down to do the time trial (29 June) and the road race (1 July).