A five-man breakaway attacked from the start, opening up a lead of five minutes, but they were caught with a few kilometers remaining.
The 28-year-old Froome took the yellow jersey on Saturday with a devastating attack on the last climb of the first Pyrenean stage and then successfully defended it the following day in the face of attacks from his rivals.
He stays 1 minute, 25 seconds ahead of Valverde, while Contador is 1:51 behind in sixth.
Froome finished last year’s Tour time trial in second place behind Wiggins. However, this time none of his main rivals is as quick as him and they face serious time losses.
“With other general classification riders, I don’t think they really like these kind of time trials,” Froome said. “I should be able to hold on to my advantage and maybe get some more time. “
Following the time trial, there will be two flat stages before the Tour heads back to the mountains.
There have been several crashes so far and there were a couple of minor ones on Tuesday as the pack hurtled toward the finish line.
The first brought down two riders as the peloton split in two going around a roundabout, and another two fell after locking bikes slightly further on. All of them hopped back on their bikes and continued.
“Every day you get through with the yellow jersey is a blessing,” Froome said. “So I’m happy just to tick that one off.”