23-year-old Almeida felt bad during the night and a positive test was taken in the morning.
He also got rid of the white youth jersey (skier under 26 years).
He was 1.54 behind leader Richard Carapaz when he was forced to break.
- We got the tough news that Joao could not start but were motivated to go for the stage victory, says the sprint specialist from the same stable, UAE Team Emirates, Fernando Gaviria.
The Colombian, however, had to settle for ninth place.
The flat stage over 156 km between Borgo Valsugana and Treviso was as made for the sprinters but a break of four skiers managed to keep out and the Belgian Dries De Bondt won the stage.
Panic when second Hindley went on puncture
It looked dramatic when overall runner-up Jai Hindley rolled into goal with a punctured tire some distance after the cluster of Carapaz but the incident occurred less than three kilometers before goal so the Australian had to credit the time from the group he went with the puncture and lost nothing but according to the stall arose for a moment of "panic" before gaining control.
Hindley is still three seconds behind Carapaz who are chasing their second overall victory after the first 2019.
- I want to keep the pink leader jersey until the end.
I trust my legs, says Carapaz.