It was the first victory in a Grand Tour for Almeida, who flew less than five kilometres from the finish with the winner of the 2018 Tour de France.
Unable to keep up with his two main rivals for the overall victory, Slovenian Primoz Roglic (Jumbo-Visma) finished third and conceded nearly 30 seconds with the bonuses.
The Frenchman Thibaut Pinot, dropped at 9 km from the finish, is one of the other big losers of the day and finishes at 3:26 of the winner, seeing his hopes of podium fly away.
His teammate at Groupama-FDJ, Bruno Armirail, gave up only a few hectometers before him after having long stood up to the best in the interminable final climb. The Frenchman conceded more than four minutes and logically gave up his pink jersey.
Wearing the pink leader's jersey at the start of the 16th stage of the Giro, Bruno Armirail cracked in the final ascent of Monte Bondone on May 23, 2023 and downgraded to 7th place in the provisional © general classification Luca Bettini / AFP / Archives
Geraint Thomas, who lost a new teammate after Frenchman Pavel Sivakov retired, had already worn the leader's tunic for four days in this Giro before abandoning it at Armirail.
In the overall standings, the British veteran, who turns 37 on Thursday, is now 18 seconds ahead of Almeida and 29 seconds ahead of Roglic.
Primoz Roglic on May 23, 2023 during the 16th stage of the Giro. The Slovenian ended up losing about thirty seconds on his rivals Geraint Thomas and Joao Almeida © Luca Bettini / AFP / Archives
A pure general classification rider, Almeida won, at the age of 24, the best victory of his career after finishing second four times in a stage of the Giro.
Renowned for his wait-and-see style, the Portuguese took the initiative this time before being relayed by Thomas.
Almeida finished fourth in the Giro in 2020 after wearing the pink jersey for 15 days, and sixth in 2021.
Last year, he had to retire because of a positive Covid-19 test on the morning of the 18th stage when he was fourth.
© 2023 AFP