Thomas will become the third British winner of the race, joining Sir Bradley Wiggins and Chris Froome, with the trio winning six of the last seven editions.
His closest rival at the start of the day, Tom Dumoulin, won the penultimate stage by one second from Chris Froome, but with Thomas only 14 seconds back the Welshman had more than enough in hand.
Thomas will carry a lead of one minute and 51 seconds into today’s traditional procession into Paris before the sprinters fight it out for glory on the Champs-Elysees.
Thomas was embraced by his wife Sara and Team Sky principal Sir Dave Brailsford at the finish, and wiped away a tear.
“I can’t believe it,” Thomas said. “I’m welling up. I don’t know what to say. It is just overwhelming. I didn’t think about it all race and suddenly I won the Tour.”
Speaking of yesterday’s stage, he said: “I felt good, I felt strong, I felt really good actually. I was maybe pushing a bit hard sometimes.
“Nico (sports director Nicolas Portal) told me to just relax, take it easy and just make sure I win the tour, and that’s what I sort of did.
“It’s just overwhelming. I can’t speak man. It’s just incredible. I believed I could beat the guys here but to do it on the biggest stage of all over three weeks, it’s insane.”
Froome, who came here looking for a record-equalling fifth Tour title and seeking a rare Giro-Tour double, had to settle for third place overall, taking back the final podium spot from LottoNL-Jumbo’s Primoz Roglic with his second place on the day.
Though it is not what he set out for, Froome said he was happy after 13 months which have seen him win all three Grand Tours on the bounce but also face a nine-month battle to clear his name after returning a test with high levels of salbutamol at La Vuelta last year. He was cleared on the eve of the Tour. “I’ve had a difficult year,” Froome said. “I didn’t think it was possible to get on the podium so I’m very happy about that.”
There was brief confusion when the timing splits appeared to show Froome had beaten Dumoulin by one second to take the stage, though it was soon corrected.
Thomas emulates Wiggins in converting himself from an Olympic team pursuit champion into the winner of the world’s biggest road race.
The 32-year-old had never before finished in the top 10 of a Grand Tour. In his only previous serious attempt to win one, he was forced to withdraw following a crash midway through last year’s Giro d’Italia.
Intermittent rain, the first significant downfall of the entire Tour, created unpredictable conditions on yesterday’s 31-kilometre course.
There was one significant scare for Thomas with around 19km to go when the bike almost slipped from underneath him on a right-hand bend.
Thomas may have known he had a buffer to play with, but he was not taking it easy as he was fastest through the first and second splits before grinding up the Col de Pinodieta and dropping back.
Irishman Dan Martin shipped more than two minutes in the time trial, but the UAE Team Emirates rider – named the most combative in the Tour overall – did enough to protect his top 10 place as he is set to finish eighth overall.