Just 0.021s separated the two Ferrari drivers, however Vettel's second hot lap, which was set to see him improve, was interrupted by Valtteri Bottas at the final corner, who moved off the racing line too late.
Moments before that, on the approach to the final corner, Bottas also got in the way of his teammate Lewis Hamilton.
Both of the Silver Arrows were fifth and sixth after the session, with Bottas leading Hamilton by just over half a tenth of a second.
In third place was Max Verstappen, setting a time that was just over a tenth down on pace-setter Vettel.
The session was not underway long before a red flag was deployed due to a crash for Robert Kubica. At Turn 2, the Williams driver found himself facing the wrong way after getting into a spin, before coming to a halt after hitting the outside barrier.
There were also issues for Pierre Gasly, as the Frenchman was forced to pull over to the side of the track in the final 20 minutes, with smoke flowing out of the rear of his car.
The second Toro Rosso driver of Daniil Kvyat also ended the session with problems, as he slid off the circuit at the final corner and lightly tapped the barrier - the Russian was told to quickly jump out of the car due to a fire that sprouted at the rear.
After his FP1 session ended in the barriers, Alexander Albon concluded the second session in ninth place in front of Carlos Sainz who rounded out the top ten.
Bahrain International Circuit - Winter testing