The Welshman's rivals for cycling's most prestigious prize, which include teammate Chris Froome in second place, mostly held back over the hilly Stage 15 with a decisive final week of racing ahead.
Thomas kept the overall lead for a fourth consecutive day before the race pauses for riders to rest on Monday.
That break will precede a stretch in the Pyrenees that will feature three mountain stages before an individual time trial on the Tour's penultimate day.
"There are three big, big days left, and then the time trial, so (I) just take each day as it comes and we will see what happens," Thomas said.
Thomas maintained his advantage of 1 minute, 39 seconds over defending champion Froome. Tom Dumoulin, the world time trial champion, remained third at 1:50 back. Primoz Roglic was fourth at 2:38 behind and Romain Bardet 3:21 behind in fifth.
With Froome seeking a fifth Tour title, Team Sky has yet to declare its current top option for the title since Thomas won back-to-back summit finishes in the Alps.
So far, Thomas and Froome have not attacked each other, but that uneasy truce could be put to the test as the race enters its decisive phase.
Thomas, while not saying he will race against Froome, has made it clear that he is not going to relinquish his shot of winning a first Grand Tour.
"I think I would have to have a bad day," Thomas said. "It's a massive honor just to be wearing (the yellow jersey), but like I have said from the very start, who knows what lies just around the corner?"
Thomas, Froome, and the rest of the overall contenders slowly rolled across the finish line at Carcassonne and its medieval city walls 13 minutes after stage winner Magnus Cort Nielsen of Denmark.
Cort Nielsen claimed his first career win at the Tour after staying ahead of Ion Izagirre and Bauke Mollema in a sprint over the final 200 meters. He finished the hilly 181.5-kilometer (112.7-mile) leg from Millau that ended in a long descent to Carcassonne in 4 hours, 25 minutes.
"I always kept a little back so I was able to respond if they attack," said the 25-year-old Cort Nielsen, who gave Astana back-to-back wins the day after teammate Omar Fraile claimed Stage 14.
The only sustained attack against Thomas came from Daniel Martin, who is 10th at almost seven minutes behind. He tried a getaway while going up the Pic de Nore climb at 40 kilometers from the finish but was reeled in on the way down.
There was also a half-hearted and short-lived attempt by Bardet to slip away on a downhill.
"We were always in control," Thomas said. "We were always in the right place, and it's a good day to get done."
Thomas and Froome lost one of their support riders for the rest of the way after Gianni Moscon was expelled by race organizers for apparently hitting Elie Gesbert of Team Fortuneo.
A breakaway group of 29 riders- none of which posed a threat to Thomas' overall lead- got away early.
Cort Nielsen, Izagirre and Mollema dropped the five other remaining escapees before disputing the stage win among themselves. With all three riders sizing one another up, Cort Nielsen stayed in front of the other two when they broke into a sprint.
Rafal Majka was leading the race on the final ascent when he barely avoided a fan who appeared to be pushed onto the road. The man was then almost hit on the back by an authorized motorbike following Majka.
Serge Pauwels of Dimension Data was knocked out of the race after breaking his right elbow in a crash near the end.
The racing returns on Tuesday with Stage 16, a 218-kilometer mountain trek from Carcassonne to Bagneres-de-Luchon.
AP writers Andrew Dampf and Ciaran Fahey contributed.
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