Howell needed a birdie on the par-five 18th for victory but sent his lengthy first putt from off the green seven feet past the hole and his par attempt missed tamely on the low side to hand Wu the China Open title in front of a delighted gallery.
Wu, 29, twice a winner on the Japan Golf Tour, joined Liang Wenchong and Zhang Lian-wei as Chinese winners of European Tour events after the duo claimed previous editions of the Singapore Masters.
"Its a wonderful day today. Everyone knows how tough it was," Wu said after finishing the tournament on nine-under par.
"I played very good today. Its very special for a Chinese winner of the China Open. Very exciting."
The duo had started the day in a four-way tie for the lead with China's Li Hao-tong and Alexander Levy but Wu's round of one-under-par 71 on the tricky Shanghai Pudong course was enough for victory in the 20 million yuan (£2.1 million) event.
Howell, playing in the final group, had led for much of the final round but a bogey-five on 14 dropped him in a tie with Wu before his disappointing final hole, where a wayward second from the fairway made his approach to the green much tougher.
Defending champion Levy (71) began his round with a bogey and a double-bogey five at the eighth left him with too much to claw back and he settled for a share of third on seven under.
Talented teenager Li finished in a share of sixth after struggling on the final day at his home event, one of four tournaments the country will host on the European Tour this year.
Argentine Emiliano Grillo looked set to post the clubhouse target after racking six birdies in his round to take him to nine-under but a costly double-bogey five at the penultimate hole left him in a share of third after a 69.
(Writing by Patrick Johnston in Singapore; Editing by John O'Brien)
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