Froome, however, celebrated the stage and general classification time gains. He put 57 seconds into his nearest rival Vincenzo Nibali (Bahrain-Merida), who now sits second overall at 1-58.
"The time trial was a bit of a strange one because I was just riding at the speed that I felt best," Froome said.
"I wasn't getting that many time checks from the car so I didn't really know where I was. I presumed it was not good news because I wasn't getting the numbers. I was a bit worried and only coming into the last six or seven kilometres, did I find out that I was on track to fight for the stage.
"It's a really big relief and I'm super happy to be in this position."
Froome won by the 40.2km stage, his second stage win of the race, in 47 minutes, 29 seconds ahead of second-placed Wilco Kelderman (Team Sunweb).
Watch: Vuelta a España stage 16 highlights
"It's an amazing feeling and I've added to my lead. To be into this position with four days of big racing left… I'm just going to take it one day at a time," he added.
"A massive thanks to the support team because they are huge part of being able to do what I'm doing. Just that support structure and having everything there to focus on the job at hand."
Froome sits in top position with only four big mountain stages to come. Wednesday's stage 17 finishes atop Los Machucos, a fearsomely steep climb with ramps of up to 31 per cent.
"It's going to be brutal, absolutely brutal. There are parts with 20 to 25%. The climb is a wall.
"You have to look at the general classification and Vincenzo Nibali is the closest. Lopez has won a couple mountain stages and I would imagine that he would be very aggressive tomorrow but he is quite far down on the general classification. I am more concerned with the Nibali and Kelderman in third place."
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