Welshman Thomas accused AG2R La Mondiale of lacking decorum after he suffered a puncture on the descent of the Col des Saisies with around 40km left of the closing stage, won by fellow Brit Adam Yates of Mitchelton-Scott.
He was a minute behind when he got a fresh wheel as AG2R turned on the gas at the head of the peloton apparently aware of Thomas' plight.
Thomas managed to close the gap on the peloton within 15km, but was far from happy with the conduct of AG2R as he informed Romain Bardet when he caught up with the French rider.
Key Moments - Stage 7: Double puncture for Thomas and late drive from Yates
"When we finally got back, after a bit of a chase, a few of the guys – (Adam) Yates, Dan Martin and (Bob) Jungels – said the same thing, that they saw it, that someone went on radio and they started sprinting," said Thomas.
I just went up to them and said thanks for that. I'm not one to hold a grudge but I also certainly won't forget it.
Geraint Thomas suffers flat tyre in Critérium du Dauphiné
For his part, Bardet denied any wrongdoing, insisting they were only riding hard to win the stage.
"We were in the process of riding, and we weren't going to stop at the first puncture," said Bardet.
That's racing. We didn't accelerate, we maintained the same pace. I explained to Geraint that of course, we're riding hard to win the stage.
Bardet was supported by his team manager Vincent Lavenu, who added: "We'd already been riding for 10 kilometres.
"We weren't going to stop and wait for them. That's only logical."
- 1. Adam Yates (GBR) Mitchelton - Scott 3:51:34
- 2. Daniel Navarro (ESP) Cofidis, Solutions Crédits +4
- 3. Romain Bardet (FRA) AG2R La Mondiale +9
- 4. Emanuel Buchmann (GER) BORA - hansgrohe +14
- 5. Geraint Thomas (GBR) Team Sky +19
- 6. Daniel Martin (IRL) UAE Team Emirates +24
- 7. Damiano Caruso (ITA) BMC Racing Team "
- 8. Guillaume Martin (FRA) Wanty - Groupe Gobert +28
- 9. Pierre Latour (FRA) AG2R La Mondiale +35
- 10. Pierre Rolland (FRA) Team EF Education First - +41
- Drapac p/b Cannondale
- 1. Geraint Thomas (GBR) Team Sky 24:43:12
- 2. Adam Yates (GBR) Mitchelton - Scott +1:00
- 3. Romain Bardet (FRA) AG2R La Mondiale +1:47
- 4. Daniel Martin (IRL) UAE Team Emirates +2:35
- 5. Damiano Caruso (ITA) BMC Racing Team +2:44
- 6. Emanuel Buchmann (GER) BORA - hansgrohe +3:05
- 7. Pierre Latour (FRA) AG2R La Mondiale +4:05
- 8. Pierre Rolland (FRA) Team EF Education First - +4:22
- Drapac p/b Cannondale
- 9. Daniel Navarro (ESP) Cofidis, Solutions Crédits +4:31
- 10. Ilnur Zakarin (RUS) Team Katusha - Alpecin +4:45