Almeida has attacked with 30 kilometres remaining in the race with Simon Yates (Team BikeExchange), Pavel Sivakov (INEOS Grenadiers) and Mikel Landa (Bahrain Victorious) for company. The premium quartet were never given much leash by the peloton, but managed to come into the final climb to the finish with 20 seconds advantage.
The final climb was 7.5km, with an average grade of 3.5 per cent, but it started at 2 per cent and gradually kicked up to 5 per cent near the last two kilometres and into Chiusdino.
Almeida attacked with just over a kilometre to go and while the rest of his breakaway companions were swept up, the revelation from the Giro d'Italia last year looked a chance to hold the pack off.
Geraint Thomas (INEOS Grenadiers) set a fierce pace at the head of affairs before Alaphilippe launched his surge for the finish line, immediately gaining lengths on the rest of the field.
Van Aert and van der Poel managed to close the gap to the world champion, but they couldn't pass him before the finish and Alaphilippe's well-timed acceleration netted him the victory.
"I was focused on keeping my position and it was a perfect situation for us, with João Almeida [up front], and for me to follow the attacks in the final kilometres," Alaphilippe said.
"I kept my position in the front with the help of Kasper Asgreen and Zdenek Stybar, and we saw João as going full gas in the last kilometre, so I was focused on what was happening behind me and everyone was on the limit. When I saw João, I went full gas. This victory makes me really happy."
The win is Alaphilippe's first of the 2021 season, coming after he was beaten out for the Strade Bianche win by van der Poel.
"This first victory of the season is a relief for me," said Alaphilippe. "It’s never easy to win in the rainbow jersey and to do it at this race feels amazing.”
Australian Robert Stannard (Team BikeExchange) was active in the finale, sprinting to sixth on the day.
