The former champions said that a thorough inspection of the new FW40 car overnight had revealed some damage to the chassis.
"Therefore, on safety grounds, the team will not run the car today," a statement said.
"A second chassis will be prepared at track this afternoon, as originally planned, with the team aiming to be back on track for the second test next week starting on Tuesday."
Brazilian Felipe Massa had been due to be in the car on Thursday, with the Circuit de Catalunya watered overnight for a wet tyre testing session.
Stroll, 18, will be making his Formula One race debut in Australia on March 26 as the youngest and least experienced driver on the starting grid.
Although he completed 98 laps on Wednesday before his accident, the only Canadian on the grid has now brought an early halt to two of the team's three days of testing and forced the abandonment of another.
On Tuesday the Canadian had spun into the gravel after 12 laps, damaging a front wing that the team could not replace without sending it back to the factory in England overnight by private jet.
The new-look cars are harder to handle and considerably faster than last year's due to aerodynamic rule changes and fatter tyres.
Triple world champion Lewis Hamilton said on Wednesday he felt for any rookie coming into the sport this year.
"It is the toughest year to come into Formula One, being that these are the fastest and most physical cars and such a short amount of testing," the Briton told reporters when asked about Stroll's mishap.
"Last year's car is easy compared to this year's car."
(Editing by Amlan Chakraborty)
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