Gunther lapped the 2.4km circuit in the Indonesia capital in 1m08.946s towards the end of the 30-minute session, edging out his team-mate Edoardo Mortara by 0.191s to claim the top spot.
The two Maserati MSG cars were quick from the onset, with Gunther setting the early pace on a 1m10.811s and Mortara backing up his team-mate in second.
A number of drivers then enjoyed stints at the top of the times as the track rubbered in, including DS Penske pair Stoffel Vandoorne and Jean-Eric Vergne, before Pascal Wehrlein broke the 1m10s barrier in his Porsche to put himself ahead of the competition.
The Maserati duo responded with Mortara setting a 1m0.538s flyer before Gunther moved even further clear of the opposition with a 1m09.263s.
Some more last-minute improvements followed, with Gunther’s final effort of 1m08.946s securing him the fastest time in the first of three practice sessions this weekend.
Vandoorne managed to briefly separate the two Maserati cars, but Mortara’s last-gasp attempt helped the Monaco-based team complete a 1-2 finish by 0.006s.
Jaguar’s Mitch Evans stood down in 20th going into the final 10 minutes of practice, but a series of quick laps propelled him to fourth at the flag, 0.342s down on pacesetter Gunther.
Porsche’s Pascal Wehrlein, who hasn’t finished on the podium since his double win in Diriyah back in January, was fifth-fastest with a time of 1m09.556s.
Jake Dennis was classified just 0.014s behind in sixth in his Porsche-powered Andretti car, while Sam Bird was another tenth adrift in sixth in the second of the two Jaguars.
Eighth place went to Porsche’s Antonio Felix da Costa, while the top 10 was rounded out by Vergne and Envision driver Sebastien Buemi.
Buemi’s team-mate and championship leader Cassidy was angry over team radio after running out of time to complete another flying lap, ending up more than a second off the pace in 17th.
Andretti's FE debutant David Beckmann, replacing Andre Lotterer who is on World Endurance Championship duty with Porsche's LMDh squad at the Le Mans test day, finished just behind Cassidy in 18th.
His fellow rookie Roberto Merhi was 21st among 22 drivers after receiving a last-minute call to replace Oliver Rowland at Mahindra.
Merhi had a lock up at Turn 1 in a session that went without any major disruptions.
