Almeida (UAE Team Emirates) launched his attack with around five km remaining and beat Thomas in a two-man sprint to earn his first Giro stage win after a mountainous 203-km route that totalled over 5,000m of elevation gain.
Almeida and Thomas took the fight to race favourite Roglic, who crossed the line 25 seconds off the pace in third.
"A special victory, a dream come true," said Almeida, who climbed to second in the overall standings.
"I worked together with Thomas to put seconds between us and Roglic, but then my main goal was the stage win. I try to improve day by day to become the best version of myself."
Ineos Grenadiers rider Thomas, who lost the overall lead to Bruno Armirail on Saturday, leads Almeida by 18 seconds in the general classification, with Roglic third at 29 seconds back.
"It was a very tough day, a lot of climbs," Thomas said. "I am happy with how it went. I found myself in front with Almeida, he was better in the sprint.
"I am not surprised by him, he is a very strong rider and a strong pretender for the maglia rosa."
Ineos, who have already lost Tao Geoghegan Hart to a fractured hip and Filippo Ganna to COVID, suffered another blow when Pavel Sivakov abandoned the race midway through Tuesday's ride, which began at Sabbio Chiese.
Sivakov was injured in the crash that ended Geoghegan Hart's race on Stage 11. His withdrawal leaves Thomas with only four support riders in the final week.
Wednesday's stage 17 is a 195-km route from Pergine Valsugana to Caorle.
