A 1m55.436s lap of Losail with just over two hours of the session to go allowed Vinales to edge out Ducati rider Andrea Iannone by 0.072 seconds and Wednesday pacesetter Jorge Lorenzo's Yamaha by 0.099s.
Vinales, who had also been quickest for a day in the previous test at Phillip Island, lapped 0.016s faster than Lorenzo had when leading the way on Wednesday.
Lorenzo had spent a couple of periods on top early in the evening before being edged back to third.
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As had been the case earlier in the week, there were few improvements in the closing hours as cooling conditions left riders anxious over the possibility of dew building up on the circuit. Vinales' time therefore stood until the flag at 11pm local time.
It was another troubled day of testing for Honda.
Marc Marquez briefly went quickest on an early run, after few had ventured out in the daylight hours, then promptly crashed at Turn 1.
He was unhurt and returned to the track half an hour later, but was left back in ninth on the timesheet, albeit within six tenths of Vinales' pace.
Dani Pedrosa was only seventh on the fastest Honda, with Valentino Rossi splitting him from his team-mate. Rossi spent a spell second to team-mate Lorenzo before a flurry of improvements elsewhere demoted him.
Ducati had a strong night. While Iannone's second place was the headline result, his factory team-mate Andrea Dovizioso claimed sixth and satellite Desmosedici riders Scott Redding and Hector Barbera were fourth and fifth for Pramac and Avintia respectively.
Aleix Espargaro filled the final top 10 spot on the second Suzuki. Both he and team-mate Vinales tried the team's new seamless shift gearbox during the session.
Pol Espargaro was just outside the top 10 in 11th and had a crash late on.
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