Sainz crashed early in the session as he passed the pit exit, bringing out the first of two red flags that greatly reduced the track time available for all drivers, with Nico Hulkenberg causing the second.
Having picked up a 10-place penalty for requiring an extra energy store after his water valve cover incident in FP1 in Las Vegas last week, Sainz hasn't suffered the same fate in Abu Dhabi.
Ferrari was planning to change his power unit and gearbox overnight anyway to previously used, but fresher, examples and thus continued with the routine swap.
A penalty could have had a crucial impact on Ferrari's battle for second in the championship, with the team and Mercedes separated by just four points.
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"For some reason, there's been a change in the track compared to other years," said Sainz of his accident.
"There are two bumps, one at the exit of Turn 2, and one at the entry of Turn 3, that with this new generation of cars it's upsetting the car a lot.
"It nearly caught me out in FP1, I changed a few things in the set-up and in the line trying to get rid of it.
"And then for some reason again, in that lap, it surprised me. It must have been an angle or exactly a way that I took the bump, and it made me a passenger from there on.
Source: Autosport