Yates finished 35 seconds behind overall winner Tadej Pogacar after his rivals slowed up to allow him to be treated for cuts to his face.
There appeared to be a tangle between the Ineos riders in the peloton with about 40km to go with Yates landing face-first on the tarmac.
The collision happened on a straight stretch of road as Yates and several of his teammates and riders from other teams fell around him.
Pogacar, the 2020 Tour de France winner, had to take evasive action to avoid becoming a casualty as well.
Ineos’ Daniel Martinez was also caught up in the crash and had to abandon the race before the end of the stage.
The 28-year-old Yates was checked by Ineos’ team doctor on the road before getting back on his bike and continuing while having cuts dressed by the race’s medical car.
Ineos confirmed post-race that Yates was taken to hospital for further precautionary checks, confirming that he had sustained cuts and bruises to his face, but had not suffered any more significant injuries.