But Thomas also says it was "never awkward" between him and his team-mate and is confident they can continue working together.
The 32-year-old Welshman went into the race having never won a grand tour, while Froome was the defending champion looking to win the Tour for a fifth time.
Thomas has written in his upcoming book 'The Tour According G' that he was told only Froome would be protected in the team time trial on stage three.
Thomas claims he was told he would be left by the other riders if he suffered a puncture or crash during the stage, despite his 52-second advantage over Froome in the general classification.
"But it's not a decision they took lightly. They would have thought about it and debated it. I said my bit, and they said, 'No.' So you have to accept it.
"The likelihood (of a puncture) is really slim but at the time I thought it's a s**t situation. Yeah, it dragged me down a bit, but you let it go."
The article also refers to the day of stage nine - which Thomas finished in second place in the GC, over a minute ahead of Froome - and the Welshman being told that only Froome would be able to use his air conditioning after the electricity tripped in the team's hotel.
Despite that, Thomas says things were not uncomfortable between the two riders.
"The biggest thing with Froomey was that it was never awkward," Thomas said. "He would have been gutted because he wanted to win a fifth Tour and three grand tours on the trot. But when he congratulated me he seemed genuine, and since the Tour we've had a couple of nights out."
Thomas won the Tour for the first time this summer (Getty )
Thomas, who signed a new three-year contract with Team Sky in September, says he would "love to win it again" and believes he is still improving.
And regarding the prospect of he and Froome taking part in next year's Tour, Thomas said: "The team obviously know I can do it now. So I think we'll be on a level playing field.
"I'm confident that, as long as we're honest and open, we can both go for it. I'd happily help Froomey if he got through the first block of mountains and he's strongest. I wouldn't ride against him to try to win then.
"I stayed because I feel I'm going to be the best I can be here. Going to another team is a gamble. I've only got another three big years left so I don't want to risk it.
"Obviously, in an ideal world, Froomey would just be riding for me. But I know that's not possible."