Katelyn Mallyon had O'Brien's charge towards the back of the field at the top of the straight in the 10-furlong heat, with Mark Zahra already well in control aboard Darren Weir's Gailo Chop.
With a furlong and a half to run, Gailo Chop had pulled a couple of lengths clear but Johannes Vermeer really began to motor and he was catching the ex-French-trained winner with every stride.
However, the line came just in time for Gailo Chop as Johannes Vermeer was just edged out.
O'Brien's other runner, The Taj Mahal, and the Willie Mullins-trained Riven Light were both unplaced.
Gailo Chop is now set to clash with Winx in the Cox Plate, although Weir concedes the supermare will be tough to beat.
He told www.racing.com: "He deserves his spot in the race now for sure. We'll head there now in fit order but with the way she (Winx) ran last week, you're probably going to be looking at second prize money. He deserves his spot and he's a lovely old horse."
Mallyon was thrilled with the effort of Johannes Vermeer and believes he can make his presence felt if O'Brien opts to turn him out again quickly.
She said: "He ran super. He really launched late and I think he has a really good chance next week in the Caulfield Cup."
Riven Light finished seventh and jockey Glen Boss felt the ground was too quick for his mount. He said: "He's pretty effective on wet tracks, but probably firm tracks not so much."
Hugo Palmer has set his sights on next month's Melbourne Cup after Wall Of Fire claimed a fast-finishing second in the Herbert Power Stakes earlier on the card.
Ridden by Zahra, Wall Of Fire finished with a real flourish under top weight in the Group Two heat, but ex-British runner Lord Fandango fended him off on the line.
Palmer said: "He's 31st in order and with Charlie's (Appleby) horse (Francis Of Assisi) coming out this morning he's 30th in line for a Melbourne Cup run, so we won't run again before the Cup unless we have to.
"We were thinking of running in the Caulfield Cup but you saw how he races today and in a Caulfield Cup, he would have got an awfully long way back, so we're happy we ran and very happy with the way he ran.
"It gives us a great deal of confidence looking into the spring."
Appleby's Kidmenever finished eighth but was diagnosed as having exercise-induced pulmonary hemorrhage (EIPH) and the thumps after the race.
Palmer was also represented in the Group One Toorak Handicap by Mask Of Time, who only made the line-up on raceday morning following a non-runner.
He turned in a fine effort though, finishing fourth as Weir completed a big-race double with Tosen Stardom.
Jane Chapple-Hyam's Kaspersky also contested the mile heat but dropped away at the finish after racing prominently.