Reigning Moto2 champion Acosta, who will ride a GasGas Tech3 KTM in his debut season in MotoGP, posted the quickest time of the three days of running on the final session on Saturday.
The Spaniard's 1m58.189s was 0.066s faster than KTM test rider Pol Espargaro and over two tenths quicker than Johann Zarco on the top Honda bike.
MotoGP's shakedown was usually reserved for test and rookie riders, but this year's concession rules have allowed Honda and Yamaha to use their race riders, meaning Zarco was joined on track by fellow racers Fabio Quartararo (Yamaha), Joan Mir (Honda), Alex Rins (Yamaha), Luca Marini (Honda) and Takaaki Nakagami (Honda).
Acosta, using KTM's carbon chassis on the two bikes he rode during the day, suffered a number of minor accidents on his way to the fastest time, which was seven tenths slower than last year's pole position time, set by world champion Francesco Bagnaia.
Acosta's time, however, was quicker than the fastest lap time in the Sepang race.
Yamaha's Quartararo finished fourth fastest ahead of KTM tester Dani Pedrosa and Mir, the quickest of the two works Honda riders. Team-mate Luca Marini, who replaces Marc Marquez at the Japanese squad, wound up eighth behind the second Yamaha, ridden by Rins.
Only one rider, Lorenzo Savadori, represented Aprilia on track on Saturday, but the Italian rode six different bikes on his way to the 12th fastest time of the day.
The final day of running was cut short by around two hours as a result of a heavy storm hitting the track.
The official pre-season test kicks off at Sepang on Tuesday and runs until Thursday.
| Pos. | Rider | Team | Time/Gap | Lap |
| 1 |
 Pedro Acosta
|
 Tech3 |
1'58"189 | 33 |
| 2 |
Pol Espargaró |
KTM test team |
+0"066 | 26 |
| 3 |
 Johann Zarco
|
 LCR Honda |
+0"211 | 39 |
| 4 |
Fabio Quartararo
|
 Yamaha |
+0"249 | 38 |
| 5 |
Dani Pedrosa
|
KTM team team |
+0"289 | 32 |
| 6 |
 Joan Mir
|
Repsol Honda |
+0"328 | 47 |
| 7 |
Alex Rins
|
Yamaha |
+0"354 | 37 |
| 8 |
 Luca Marini |
Repsol Honda |
+0"746 | 46 |
| 9 |
 Cal Crutchlow
|
Yamaha test team |
+0"794 | 54 |
| 10 |
 Takaaki Nakagami
|
LCR Honda |
+0"883 | 44 |
| 11 |
 Michele Pirro
|
 Ducati test team |
+1"141 | 37 |
| 12 |
Lorenzo Savadori
|
 Aprilia test team |
+1"811 | 68 |
| 13 |
 Stefan Bradl
|
Test team Honda |
+2"910 | 14 |
