The Malaysian's win was a stunning reposte after failing to reproduce his 2010 form in Singapore last week where he was beaten in the last eight. In Jakarta he dropped only one set to Kenichi Tago, the All England Badminton Open finalist.
Chong Wei had previously gone 17 matches unbeaten after lifting the Korean, Malaysian and All England titles.
With five of the 10 Super Series titles decided, Chong Wei has cleaned up in four of them.
The Malaysian Datuk will now head to the World Championships in Paris as favourite, though Lin Dan, his Chinese rival, didn't participate in the last two events in Indonesia and Singapore.
"I worked my socks off to win the first game. Once I achieved that, I felt confident I would win the second," Chong Wei said.
Hidayat, who had previously won seven Indonesian Open titles, reflected: "This physical up and down is normal in sports which can affect our performance but then we cannot be at the top all the time."
http://www.telegraph.co.uk/sport/othersports/badminton/7857830/Malaysias-Lee-Chong-Wei-defeats-Taufik-Hidayat-to-lift-Indonesia-Open.html