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Jun Hao will face either Chou Tien-chen or Lin Chun-yi, both of Chinese Taipei, in the last-16.
World No 32 Jun Hao showed determination and resilience to win the first set with relative ease in 16 minutes, with world No 3 Jonathan making numerous unforced errors despite the partisan crowd rooting for him in Jakarta.
However, Jun Hao, who was leading in the second set until 15-11, allowed Jonathan to crawl back and level the score at 15-15.
The Malaysian even lost two challenge calls within two minutes.
Buoyed by the vociferous home crowd, Jonathan raced ahead to win the second set to force a rubber game.
Jun Hao came back strongly in the third set and showed accuracy, taking an 11-5 lead in 12 minutes.
Jonathan attempted a comeback and reduced the deficit to 8-12, but Jun Hao shifted gears before going on to win the match.
This was the first meeting between the two players.
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