Thomas, who had two punctures, ended the stage in fifth place, but the Welshman stayed one minute ahead of Yates in the general classification of what is the final warm-up race for the Tour de France.
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.
England star open to Tottenham Hotspur exit
Ruben Loftus-Cheek will challenge for a starting place but Alli is expected to begin against Tunisia in Volgograd next Monday. Recalling his outing for Spurs against Real Madrid in the Champions League, singling out his height and ability to play.
"Without the boys here I would not have won the Dauphine". "I'm more anxious about my form for the Tour de France. I explained to Geraint that of course, we're riding hard to win the stage".
Yates said: "The Tour de France has been my main goal for the whole season".
It was Thomas' second World Tour stage race win after he won Paris-Nice in 2016.
Nick Jonas and Priyanka Chopra attend his cousin's wedding
The couple seemed to have a great time making videos of the wedding on their cellphones and chatting with his relatives. Taking Priyanka as "plus one" most certainly proves that the singer took the actress as his "date" for the wedding.
Thomas would normally expect to be a domestique for four-time champion Froome at the Tour but victory at the Criterium against potential Tour contenders, coupled with the uncertainty surrounding Froome's adverse analytical finding from a drug test past year, means the Welshman could yet be riding for his own glory next month.
"From the start of the year I said I wanted to get there [the Tour de France] in the best shape possible and I'm on course for that".
After catching up with the main leaders with 30km remaining, he crossed the line a handful of seconds off the pace without ever being in danger of losing possession of the yellow jersey. Romain Bardet (FRA) AG2R La Mondiale +9 4. Emanuel Buchmann (GER/BOR) 14, 5. Daniel Martin (IRL) UAE Team Emirates +24 7. Pierre Latour (FRA/ALM) 35, 10.
Griezmann is staying in Spain, that much is clear - Deschamps
Lemar was strongly linked with both Liverpool and Arsenal last season but is now set for a move to the Wanda Metropolitano. However, those figures will revert to the previous numbers after July 1.
Thomas now leads Yates by 1:29 in the overall standings.