The Bahrain Grand Prix victor did not take part in the final 15 minutes of the second hour-long session after he damaged the front-left track rod on his F1-75 challenger.
He clipped the inside wall passing through Turn 4 and had to abort the Turn 5 sweeping right hander before cruising back to the pitlane for repairs.
But that only came after his soft tyre run to wrest back the FP2 lead from Verstappen, Leclerc ultimately pipping the Dutch racer by 0.14s thanks to a 1m30.074s flier.
Immediately prior to second practice, drivers and team principals were called to a meeting with F1 CEO Stefano Domenicali and motorsport director Ross Brawn.
This was held following the missile attack on the nearby Aramco distribution station during FP1, for which Yemeni rebel group Houthi has claimed responsibility.
This is reckoned to be the same organisation whose missiles were intercepted close to the 2021 Formula E season opener in Diriyah.
As a consequence of the meeting, the start of FP2 was delayed by 15 minutes to 20:15 local time with only Sainz and Valtteri Bottas initially filmed ready in the garage.
It was Alfa Romeo driver Bottas and his rookie teammate Zhou Guanyu that hit the Jeddah Corniche street circuit first to lead a flurry of cars and leave only the Red Bulls in the pits.
Bottas was immediately on the pace, picking up from his third place in first practice, by setting an initial 1m31.802s banker on the popular C3 medium tyres.
Esteban Ocon was next over the line aboard the Alpine but was 0.7s adrift as Zhou ran another 1.7s slower than his stablemate before the Ferraris came to the fore.
Sainz also used the yellow-walled Pirelli tyre to bolt to the top of the leader board with his first effort buzzing the timing line at 1m31.382s to run four tenths clear.
But he was soon after deposed by stablemate Leclerc, as the points leader was the first driver to dip into the 1m30s.
Leclerc’s 1m30.216s lap on the C3s four minutes into the session gave him 1.1s in hand, despite initial oversteer as Sainz complained about porpoising rearing its head.
Leclerc then turned in two highly consistent follow ups, lapping within 0.15s of his personal best as he topped all three sectors.
It was not until six minutes in that the Red Bull finally joined the session on C3s, leaving Alexander Albon, Nico Hulkenberg, Mick Schumacher and Fernando Alonso as the only drivers to ply their trade on the harder C2 compound.
The times remained stable for nearly the next quarter of an hour before Verstappen stretched the legs of his RB18 to eclipse Leclerc by just two thousandths.
After his first effort placed him 1.074s off Leclerc, the defending champion clocked a 1m30.214s to run fastest before the field swapped to the fastest available C4 tyre.
Leclerc was able to regain first place as he brought the benchmark down to 1m30.074s to find 0.14s over his Red Bull rival, also beating his own FP1 benchmark of 1m30.772s by seven tenths.
But the pace jump on the theoretically faster tyre was less than anticipated.
Lewis Hamilton was the other major climber as he rose from 14th up to fifth, behind Sergio Perez, but ahead of his Mercedes counterpart George Russell.
The seven-time champion delivered a 1m30.513s, having stopped early in the session to swap to his spare seat to sit higher in the car.
But then run plans were interrupted by a brief virtual safety car thanks to the Haas of Magnussen stopping with a power unit issue halfway round the lap to be recovered.
That ended a difficult Friday for the Dane, who landed fifth in Bahrain.
He had complained of an engine problem earlier in the session before getting the all-clear from the team to push, having not set a time in FP1 owing to a hydraulic leak.
Sainz presented the other noteworthy incident when he too clipped the wall, the Spaniard letting his car run wide and into the outside barrier on the banked Turn 13.
Behind the two Silver Arrows, Lando Norris ran to seventh for McLaren ahead of Ocon and Bottas as Yuki Tsunoda set the pace for AlphaTauri in 10th.
Behind Alonso, Pierre Gasly and Mick Schumacher, the Aston Martins sandwiched Daniel Ricciardo as Stroll grabbed 14th while substitute teammate Hulkenberg was 16th.