The Canadian lost the rear of his AMR23 exiting the final corner as he attempted to finish his final flying lap after the chequered flag had been waved for Q1.
Stroll appeared to clip the exit kerb at the first apex to unsettle the rear axle, which projected him into the outside wall.
He made heavy contact to spin across the circuit and into the path of McLaren driver Oscar Piastri, who narrowly avoided the stricken Aston Martin.
Stroll radioed to confirm he was OK before eventually exiting the car.
When Stroll did climb out, he was met with cheers and applause from the Marina Bay grandstands.
The FIA said a lengthy recovery period was anticipated given fluid was spilled on the track surface while barrier checks were required, before Q2 resumed at 9:53pm local time.
As a result of not crossing the timing line, Stroll ended the session in 20th behind Alfa Romeo driver Zhou Guanyu.
There was potential, prior to the shunt, for a big scalp to be claimed in Q1 given the heavy traffic and extreme track evolution.
As grip levels improved dramatically late on, Yuki Tsunoda ran fastest for AlphaTauri before the Haas machines of Nico Hulkenberg and Kevin Magnussen ran temporarily to second and third.
This came as the Mercedes, Ferraris and Max Verstappen struggled to improve their first and second sector times as a result of the out-lap congestion, which would have likely hindered tyre preparation.
Verstappen is also under investigation for impeding in the pit lane, having sat stationary aboard his RB19 at the exit while the green light was displayed.
Amid the drama, Lewis Hamilton and Alex Albon narrowly progressed into Q2.
Meanwhile, 16th-placed Valtteri Bottas, Piastri and Williams rookie Logan Sargeant were also eliminated along with Zhou and Stroll.
