The morning session was halted after Leclerc, who was quickest in it, and Mercedes' seven-time world champion Lewis Hamilton ran over the kerbside drain with debris thrown into the air.
Teams have only one car each on track over the three days of testing at Sakhir, with Leclerc and Sainz alternating, and Ferrari took the SF-24 back into the garage for repairs with the shutters down.
Sainz took over in the afternoon/evening session, which was brought forward an hour to make up for the time lost to track repairs, and lapped with a best time of one minute 29.921 seconds on the second softest C4 tyre.
"Another day of testing completed according to plan and without issues," Sainz said.
"We managed to go through the whole afternoon programme smoothly, combining various tests with low and high fuel runs, so it was interesting to get a feel for this year’s car in different configurations."
Red Bull's Sergio Perez was closest to him on the slower C3 tyre, 0.758 off the pace, with Hamilton third and McLaren's Lando Norris fourth.
"We've clearly made an improvement with this year's car and it's much nicer to drive," said Hamilton, who completed 123 laps.
Leclerc had topped the earlier timesheets in 1:31.750 on the C3 tyre with McLaren's Oscar Piastri 0.578 slower and Williams' Logan Sargeant third and 0.828 off the pace.
The Ferrari driver returned in the afternoon to complete his programme before handing over to Sainz.
Drain incident
The drain incident brought back memories of Las Vegas last November when Sainz ran over a loose cover during first practice, bringing a lengthy halt to proceedings.
Ironically, the Spaniard had gone out to watch Leclerc on Thursday and was standing near Turn 11 when the incident happened.
Ferrari technical director Enrico Cardile said the problem was easily fixed.
"The damage was on a small portion of the floor... nothing worrying. We changed the floor, proceeding with our plan and no drama," he added.
Sainz ended up with 84 laps to Leclerc's 54.
The season starts in Bahrain on March 2nd, the first round of what will be a record 24-race championship, and every minute of pre-season running is precious.
Red Bull's triple world champion Max Verstappen was fastest on Wednesday, although timings do not mean so much with teams running to their own programmes, and Perez had his first turn on Thursday.
The Mexican had a problem with overheating brakes in the morning but ended the day with 129 laps under his belt.
"It was unexpected to be in the car all day today but the delays meant my early runs were cut short, so the team decided to extend my day and I am back in the car again tomorrow morning," he said.
"Generally speaking, I think the RB20 is a step forward for the team and we have gone in the right direction."
