France's Garcia, the number two seed, has been in red-hot form, winning the Cincinnati Masters last month before reaching her first Grand Slam semi-final at Flushing Meadows two weeks ago.
But she came up short against world number 28 Zhang in Tokyo despite hitting 27 aces to her opponent's four and holding a match point at 5-4 in the second set.
Zhang fought back to level the match via a tiebreak before munching on a sandwich during the changeover.
It seemed to energise Zhang as she outlasted Garcia in final set, taking it on her second mmatch point when the Frenchwoman hit long after two hours and 30 minutes.
Zhang will now face either sixth seed Karolina Pliskova of the Czech Republic or Croatia's Petra Martic in the quarter-finals.
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