As Latifi returned to the track, he appeared not to spot Nikita Mazepin bearing down on him in the Haas, leading to contact and the Canadian spearing heavily into a wall.
Even during the resultant safety car period there was drama as Mazepin's team-mate Mick Schumacher lost his front wing after sliding into a wall along the pitlane as he attempted to keep heat in his tyres.
With the pitlane closed while Latifi's car was recovered, Schumacher was forced to trundle around for three laps without a nose until he could finally take a replacement.
It was also behind the safety car that Red Bull's Perez forgot the rules and was issued with an obvious 10-second penalty as he had run off track and was passed by Daniel Ricciardo and Pierre Gasly, only to decide to claim his position upon returning.
Once the race restarted, Verstappen opened up a five-second cushion to Hamilton, which had been reduced to less than two seconds by the time he pitted from inters to the compound after 27 laps.
Verstappen and Hamilton tyre change
Attempting the overcut, Hamilton was hesitant approaching his wet pit box, with his stop compounded by a slight issue with the removal of the front-right tyre.
It led to him slotting back into second behind Verstappen, and in closing the gap, he then made his error at Tosa as he attempted to lap Russell.
The 36-year-old took to the gravel, but in attempting to turn out of the problem, he crunched his front wing into a barrier.
After finally managing to find reverse and return to the circuit, and ultimately the pits for a new nose, it was then that Bottas and Russell were involved in their accident.
On the first lap, Perez made an error and dropped out of the points, and while Verstappen sailed off to victory, behind the Dutch driver, Hamilton surged to second, taking the point for fastest lap to hold a one-point lead over Verstappen in the drivers' standings.
Norris equalled his best F1 result with third, followed by Leclerc, Sainz, Ricciardo, Stroll, Gasly, Raikkonen and Esteban Ocon in his Alpine.
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