That was a fraction quicker than Wednesday’s benchmark, set by factory Ducati man Danilo Petrucci.
Nakagami was at the forefront of a late host of improvements, with Yamaha’s Maverick Vinales jumping to third around the same time with a time just 0.121s off the pace.
Jorge Lorenzo made it three Honda riders in the top four with a 1m38.105s shortly after the seven-hour mark.
Petrucci was once again the best of the Ducati runners in fifth, three places ahead of Andrea Dovizioso, who despite suffering pain after his Wednesday crash was able to take part in Thursday’s running as normal.
Splitting the two factory Ducati runners were Franco Morbidelli on the Petronas SRT Yamaha and another GP19 rider, Pramac’s Jack Miller.
Top rookie Francesco Bagnaia on the second Pramac bike and Alex Rins (Suzuki) completed the top 10.
Valentino Rossi was half a second slower than Yamaha teammate Vinales and ended the final day of 2018 running 11th, one place ahead of another rookie, Fabio Quartararo (Petronas).
Pol Espargaro was the quickest of the KTMs in 15th, four places ahead of new teammate Johann Zarco, while Andrea Iannone led the way for Aprilia in 18th.
Iannone’s teammate Aleix Espargaro made a brief appearance having sat out most of the test due to illness, but Bradley Smith spent the majority of the day on the #41 machine that was 20th fastest.
No crashes were reported in an incident-free day of running, although Ducati tester Alvaro Bautista did stop on track after running out of fuel.
MotoGP now goes into a two-month winter shutdown, with the first official pre-season test of 2019 taking place at Sepang on 6-8 February, following a shakedown for test riders on 1-3 February.