Thomas, Froome and the rest of the overall contenders finished 13 minutes behind stage victor Magnus Cort Nielsen.
"We're not looking at each other as rivals, we're looking at the other guys in third, fourth, fifth - they are the ones who could put us under pressure".
Thomas leads Froome by 1 minute, 39 seconds.
The move hurt Frenchman Romain Bardet, who ended up 22 seconds off Fraile's pace.
At the start of the day, there were no fewer than 14 teams without a stage win, and with big days in the mountains to come, many teams will have viewed this stage as the last real chance to stand atop the podium.
"For me this is the highlight of my career, it's a massive honour and privilege to be wearing the jersey and have such an incredible race so far", he said.
World champion Peter Sagan got into the breakaway, and he took third place in the day's intermediate sprint to all-but wrap up the points classification, receiving his 100th green jersey at the finish.
Thomas and the main peloton soaked up futile attacks from Irishman Dan Martin (UAE) and Rafa Majka (Bora) before crossing the finish line just over 13 minutes in arrears on what, for them, was a comparatively easy stage ahead of Monday's rest day.
"That's never going to happen so it's all about just winning this race", he added.More news: Donald Trump calls negative coverage of his Putin meeting 'fake news'
Former French cyclist Jerome Chiotti, who in 2000 admitted doping with the Festina team, compared Sky's dominant performances to those of disgraced American Lance Armstrong and his US Postal team.
"It's just how I feel".
"For sure I'm not going to sit up and lose time, but I think we're in a great position".
Moscon, a one-day race specialist who is on the Tour as a domestique, was also accused of sending another rider crashing a year ago before being cleared of wrongdoing by the International Cycling Union (UCI). Chris Froome (Team Sky) +1.39 3.
The British outfit have detractors, both stemming from their recent dominance of the sport, and because of a recent anti-doping investigation into Froome, which was dropped in early July.
"Gianni is desperately disappointed in his behaviour and knows that he has let himself, the team and the race down".
On a day when the French newspaper Liberation wrongly described Froome's recent salbutamol case as a "positive test" which was "white-washed" by the UCI, Thomas said questions about why there is ill-feeling towards Team Sky was perhaps one for the French press.
"The Tour de France is promoted as the world's greatest annual sporting event and, if you want the best worldwide riders to come to your country, maybe treat them with a little more respect", he said. "My first Vuelta, I won stages as well, so I knew that it was possible to win on your first time you're in the race".
"We accept it and we have to make a decision about how to behave - we're trying to remain dignified, we're trying not to react and we're trying not to get distracted by it", he said.