The Tony Pike-trained galloper was launched from mid-field on the home turn to deliver a flying finish to gain victory the time-honoured fixture.
Muddling early sectionals in the event led to Magic Chai recording the second-slowest Wellington Cup time, while the race has been run over 3200m, in more than 50 years.
Only Cluden Creek has registered a slower time, 3.26.49 in 2004, since 1966 winner Red Crest ran 3.27.5.Magic Chai was clocked in this year’s edition at 3.25.19.
The painfully slow tempo could have contributed to ending the winning chances of favourite and Otago hope Patrick Erin.
The horse over-raced fiercely in the race’s early stages with rider Chris Johnson standing high in his irons as he tried to restrain the Brian and Shane Anderton-trained galloper.
By the 1000m, Patrick Erin was still travelling on a tight rein before the field started to quicken for the run home.
The galloper fought bravely under his 59kg topweight in the straight but could not match the sprint showed by the race’s placegetters and ran fourth.
Magic Chai could attempt a rare cups double after rising through New Zealand’s staying ranks with his win on Saturday.
"We’ll get him home and see how he is and if his form holds up, then the Auckland Cup is an obvious target," Pike said.
"He’s only had 18 starts so he’s still pretty much untapped. He’s a good, genuine stayer."
Awapuni filly Dijon Bleu continued her brilliant season and confirmed she would step up over more distance by winning Saturday’s Desert Gold Stakes.
The Lisa Latta-trained 3yr-old delivered an explosive finish once clear in the home straight to strongly run out her first attempt at 1600m. There were questions before the race whether she could handle the distance, but afterwards jockey Leith Innes suggested 2000m was within her range.
"She gets her head up high and she’s not very big, but she’s a star," he said.
"It will be interesting to see if she gets 2000m, but I don’t see why not."
Innes rode the filly with extreme patience, electing not to push off the fence before the home turn and instead waiting for inside runs.
"I could have got out and rolling 600m from home, but I had no choice and then she exploded when she was clear."
Dijon Bleu could run in next weekend’s Karaka Million 3yr-old Classic but was more likely to have her next start in the Sir Tristram Classic, Latta said.
— Jonny Turner, additional reporting NZ Racing Desk
