Super Seth has delivered on his potential in the stallion-making Caulfield Guineas, launching home late to deny the previously unbeaten Queensland gelding Alligator Blood in the final stride of the $2 million Group One race.

Trained by Sunshine Coast-based David Vandyke and ridden by former Caulfield-based Ryan Maloney, Alligator Blood shot clear with 250m to run in Saturday's 1600m Classic for three-year-olds and looked set for victory.

But with winkers on for the first time, the Anthony Freedman-trained Super Seth ($7.50) flew late under jockey Mark Zahra and nailed Alligator Blood ($5) on the line.

It was the second Guineas of the day at Caulfield to be decided by a nose margin, with favourite Flit also winning the Thousand Guineas for fillies by the barest of margins over Missile Mantra.

Super Seth's stablemate Groundswell ($13) battled on well for third, another 2-1/4-lengths away while favourite Dalasan finished fifth.

Super Seth's triumph gave Zahra a Group One double for the day after winning the Caulfield Stakes (2000m) on import Cape Of Good Hope.

"Super Seth has always shown he had that sort of ability and the winkers obviously worked really well for him today," Freedman said.

"It's a great thrill.

"He's obviously a stallion now."

While Maloney couldn't fault Alligator Blood's performance, he said the result was "gut wrenching".

"I've never been so happy and gutted at the same time for the horse," Maloney said.

"We kicked clear from the leader and I thought I was home.

"It's a gut-wrenching result but I couldn't be more proud of the horse."

Vandyke said Alligator Blood, who was trying to emulate his 2012 Guineas-winning sire All Too Hard, just had to do a bit of work early and over-raced a touch before getting left in front a long way out.

"It was a massive effort but it does hurt," Vandyke said.

"It was very close."

Super Seth won the McNeil Stakes (1200m) at Caulfield in his spring return and connections had a decision to make whether to target the Group One Coolmore Stud Stakes over 1200m at Flemington next month or stretch out to the 1600m of the Guineas.

After he failed two starts ago in the Danehill Stakes on the straight course at Flemington, it made the decision easier and he closed strongly for sixth in his lead-up in the Prelude (1400m).

"I wasn't convinced he would run a mile," Freedman said.

"I thought we might go back to the Coolmore, but it has worked out well.

"The target was always to win a stallion race with him.

"He had a good two-year-old prep and he came back well but he needed to lift to win today. And I think the winkers obviously helped.

"The other horse was well clear and was going well. Obviously he might have just tightened up a bit late and we got him."