Bernal said compensating for his back led to some discomfort in his knee.
“I want to ride to Paris,” he added.
It was a day to forget for Ineos-Grenadiers as Carapaz had to settle for second after two brutal attacks from the breakaway group in the decisive climb had left his rivals in the red.
But Kaemna (Bora Hansgrohe), who narrowly missed out on a stage win last week when he lost a two-man sprint against Colombian Dani Martinez in Puy Mary, went solo just when Carapaz was recovering from his effort at the top.
“I didn’t want it to be another two-man sprint so when I saw Carapaz struggling a bit I thought I had to go full gas,” said Kaemna, who had also lost a two-man sprint for victory at the 2017 under-23 world championships.
“When I saw that I was gaining a few seconds it boosted my confidence and I knew I was going to win.”
All 22 teams were cleared to continue the race on Tuesday after all riders and staff members returned negative coronavirus tests.
Tuesday also marked the return on the race of Tour director Christian Prudhomme, who had returned a positive result in the previous round of testing.
Thursday’s 17th stage is a brutal mountain trek in the Alps, over 170km and ending in Meribel at the top of the Col de la Loze, 2304m above sea level.