Doohan lost control of his Alpine as he turned into the flat-out Turn 1, spinning into the gravel at 300km/h.
The impact with the barrier tore two wheels from his car and triggered the first of four red flags in the hour.
After gingerly climbing from the wreckage, Doohan visited and was cleared by the circuit medical centre.
“First of all, I am okay after the incident,” the 22-year-old said.
“It was a heavy one, something that caught me by surprise, and I will learn from it.
“I know the team has a lot of work ahead to repair the car going into tomorrow, so thanks in advance to them for their efforts.
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“My focus is on tomorrow where we will have Free Practice 3 to get ready for Qualifying.”
According to team principal Oliver Oakes, the issue was caused by Doohan failing to close his DRS ahead of turning into the right-hander.
The Suzuka circuit features just one DRS zone despite, on paper, having facility for more, located on the pit straight and leading into Turn 1 – a corner which can be taken at full throttle in qualifying trim, with the DRS flap closed.
The back straight does not feature a DRS zone given it feeds into the fearsome 130R left-hander.
“We are all relieved to see Jack walk away from his incident in Free Practice 2 and glad to see he is okay after his precautionary checks,” Oakes said.
“It was a misjudgement of not closing the DRS into Turn 1.
“It is something to learn from and I know Jack and the team will be ready for tomorrow.
“His crew will work hard to have the car prepared after the damage.”
Alpine has confirmed to Speedcafe that it is repairing Doohan’s crashed chassis rather than building up the spare tub.
Doohan managed just four laps before the incident, which occurred as he commenced his second push lap.
The Australian missed the opening hour of running as his seat was filled by Ryo Hirakawa, leaving him desperately short of laps heading into final practice on Saturday.
Across the garage, teammate Pierre Gasly demonstrated promising pace, clocking the ninth best time in Free Practice 2 having been 14th earlier in the day.
“From a performance point of view today, there are some things for us to work on,” Oakes said.
“Pierre had a good run in Free Practice 2, which bodes well for tomorrow, as did Ryo, who did a great job to run through the programme this morning.
“We tried some set-up options between cars and we have a good direction to go in ahead of Qualifying.”
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