Piastri will now start tomorrow's Singapore Grand Prix from 17th, despite being on a much faster lap than his first effort.
As he came round the last corner, he had to instinctively avoid Stroll's car whilst still flying onto the start-finish straight.
"I was in the last corner when the red flag came out," he told Sky Sports after the session.
"It wasn’t the best lap I’ve ever done, but it should’ve been enough to get through. Starting the lap, it was like driving through a car park. Bit embarrassing for everybody to be honest.
"I’m glad Lance is ok, obviously a very big crash. Just a shame we were just behind it instead of just in front of it. Makes our evening tomorrow very difficult."
It meant that McLaren were left with just one car in qualifying, with Lando Norris their only hope of maximising the performance of a car that has looked very strong so far this weekend.
McLaren CEO Zak Brown was sympathetic towards Stroll, despite his team's disappointment.
“Disappointing, happy Lance is ok," he told Sky Sports.
That was a big hit. Unfortunately, it prematurely ended Oscar’s qualifying. I think he had enough pace there to get it to the next session and I think had enough pace to be in Q3.
"Now we’ll prepare for tomorrow’s race and focus on Lando now for the balance of the session."