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Verstappen has now failed to win any of the last six GPs after claiming the honours in seven of the first 10.
Italian Antonelli, who has won one sprint and one feature race for Prema Racing in Formula Two this year, will join George Russell at Mercedes, with Hamilton switching to Ferrari.
The British team announced on Tuesday that Argentine F2 driver Franco Colapinto would replace Logan Sargeant for the remaining nine races of the season, starting with Sunday's Italian Grand Prix at Monza.
It was the first time since the race returned to the calendar in 2021 that Verstappen had not triumphed at Zandvoort and extended his losing streak this season to five races.
The 23-year-old, who has yet to score a point this year and has already lost his seat for 2025, was taken to the medical centre for precautionary checks.
The two have been together through Hamilton's 12 years at Mercedes and their radio exchanges have become part of the language of the sport for a global television audience.
Horner, whose team is currently leading both championships, had denied the accusations.
The decision means that McLaren's Oscar Piastri finishes second with Ferrari's Charles Leclerc in third.
Lewis Hamilton took third for Mercedes, his 200th Formula One podium coming despite a late collision with Red Bull's championship leader Max Verstappen, who came off worse and finished fifth.
The 39-year-old Mercedes driver's last win before Silverstone was in Saudi Arabia on December 5, 2021, and Sunday was a record-extending 104th of his career.