Thomas was hoping to defend the title he won last year but the 33-year-old Welshman has had to settle for second place behind Colombian team-mate Egan Bernal.
“He’s had a fantastic tour,” Brailsford said.
“The first time someone wins the Tour de France they hardly ever come back and perform well the year afterwards.
“Geraint’s defied all the odds there and could have won the race. He’s fair, he’s balanced, he wanted to win, but then as soon as the opportunity came for the team to win he was 100 per cent behind it and he’s just a pleasure to work with. He’s a class act.
“We’ve been very fortunate in the last couple of seasons to be in this position but every time is different and this race was the most exciting, open, topsy-turvy kind of race that we’ve ever been involved in.
“So to come away with first and second on the podium has been tremendously rewarding and of course with a guy so young in Egan it has added an extra bit of enjoyment and a different element because all our previous wins have been with British riders.”
Bernal is the first Colombian to taste victory in the Tour and, at 22, is the youngest winner in the post-war era.
“He was 19 when we first spoke to him but he was so mature for his age,” Brailsford added.
“He’s such a well-balanced, super generous, kind, very giving individual, very concerned about everyone else, and yet he’s got this incredible winning streak inside him which has made him the champion that he already is.”
“He is a lovely young man and he doesn’t hesitate at all if he sees something in the team that he doesn’t feel quite happy about.
“He’s pretty quick to come knock on my door and say I’m a little concerned with rider X, he seems a bit upset with something, I think you should sort it out.”
Brailsford revealed that four-time Tour de France winner Chris Froome is making good progress with his recovery from the horrific crash during a practice ride before stage four of the Criterium du Dauphine which left him in intensive care.
“He’s ahead of schedule,” Brailsford said. “He’s been riding his static bike with one leg, he’s managed to turn a pedal with his other leg so he’s well ahead of where he was hoping to be and he’s putting everything into his recovery so hopefully we’ll see him back at the Tour de France next year.”
On the road, Champagne glasses clinked for Bernal as the field rode to Paris before Caleb Ewan won stage 21 on the Champs-Elysees.
Australian Ewan came from well back in the pack to outsprint Dylan Groenewegen and collect his third stage win of the Tour as the sun set over the Arc de Triomphe at the end of the 130km stage from Rambouillet. Just behind, Bernal crossed the line alongside team-mate and last year’s winner Geraint Thomas to secure his first Grand Tour victory in only his second career three-week race.
Bernal, who took the yellow jersey on Friday’s weather-shortened stage 19 in the Alps, becomes the first Colombian winner of the Tour and, at 22 years 196 days, the youngest winner in more than a century.
Thomas collected second place to give Britain a 10th podium finish in the history of the race, while Jumbo-Visma’s Steven Kruijswijk secured third place.
As the traditional procession into Paris began from Rambouillet to the west of the city, Bernal was congratulated first by Julian Alaphilippe, who animated the 106th Tour as his aggressive start and dogged defence was rewarded by 14 days in the yellow jersey and, it was announced on Sunday, the Super Combatif award for the most aggressive rider.
Bernal was then handed a glass of champagne from the Ineos team car as the celebrations began, with Bora-Hansgrohe’s Peter Sagan – who won the green jersey for a record seventh time – doing his best to photobomb them as they lined up across the front of the peloton.
Bernal’s victory continues a remarkable run of success for Sir Dave Brailsford’s team, who have now won seven of the last eight Tours and – including the 2011 Vuelta a Espana title awarded to Chris Froome earlier this month following Juan Jose Cobo’s doping case – 10 Grand Tours in all since their formation in 2010.
For once Brailsford’s team did not dominate a Tour which will be remembered for Alaphilippe’s remarkable run in yellow, but they were always next in line for when the Frenchman did – as expected – finally crack in the Alps.
Although Thomas had been best placed to take over for much of the race, Bernal made moves in the Pyrenees to take back time he had lost in the time trial, and then had the best legs in the Alps when it really mattered.