
Displaying powerful smashes, Jun Hao won in straight games of 21-16, 21-19 to overcome the world No 5 in 53 minutes.
The Malaysian, ranked world No 25, had qualified for the second round yesterday when his Chinese opponent, Lei Lanxi, gave him a walkover.
After losing the first game, Jonatan came back strongly to lead 18-15 in the second game but Jun Hao took the next four points before going on to win the match.
It was his third victory over the Indonesian No 1 in five meetings.
In the quarter-finals tomorrow, Jun Hao will face a stiff test against reigning world champion Kunlavut Vitidsarn, who won the Thailand Open title two weeks ago.
He last met Kunlavut, the world No 2, at the Thailand Open last year where the homester won in three games.
Jun Hao also had an impressive run at the Singapore Open last year, defeating Kanta Tsuneyama in the first round, and causing an upset by beating two-time champion Anthony Ginting in the second round before losing to Viktor Axelsen of Denmark.