The 33-year-old, who has withdrawn from this week's Australian Open, the last major tournament before the Olympic Games, had come through one of the hardest games of his career against the Dane, said national coach Hendrawan.
"The Indonesia Open final was one of Chong Wei's toughest matches because Jorgensen was at his very best," Hendrawan told southeast Asian media.
"This win definitely puts Chong Wei on the right track in his preparation for the Olympics, with two more months to go.
"We still have to work on tactics, physical training and how to handle the pressure."
Lee returned to action in May last year after a backdated eight-month doping ban for testing positive for dexamethasone, an anti-inflammatory drug, at the 2014 world championships.
(Reporting by Nivedita Shankar in Bengaluru; Editing by Peter Rutherford)
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