In humid conditions at the Mandalika track on the resort island of Lombok, the Pramac rider clocked the best lap time of one minute and 30.689 seconds, ahead of Aprilia's Maverick Vinales by 0.221 sec.
In the title race, Morbidelli's Pramac partner Martin is going into race weekend 24 points clear of defending champion Francesco Bagnaia, who finished far back in 14th in the first practice session.
Spain's Pedro Acosta finished fourth with France's Johann Zarco in fifth.
Bagnaia's teammate Enea Bastianini and Gresini's Marc Marquez are 59 and 60 points behind Martin with six race weekends left.
They finished eighth and sixth fastest in their respective sessions on Friday morning.
Martin, 26, extended his lead over Ducati's Bagnaia last weekend after the Italian crashed out of the Emilia-Romagna MotoGP.
The second practice session, from which the top 10 riders go straight into Saturday's second round of qualifying, gets underway at 3:00 pm (0700 GMT).
Qualifying shapes the grid for both the sprint race on Saturday and the main event GP on Sunday afternoon, with a maximum of 37 points available.
