Peter Snowden's thoughts turned to his stable apprentice after Pajaro came with a late run to win the $200,000 Scone Cup.

Winona Costin was booked to ride Pajaro but she had to forfeit her rides on Friday - the first day of the Scone Cup carnival.

It was left to Tim Clark to produce the ride of the meeting to get Pajaro to win for the first time in almost a year.

"It's just a bit of a disappointment for Winona," Snowden said.

"She was supposed to ride the horse today and she wasn't well this morning."

As Clark chanced his arm from a wide barrier, Pajaro threaded his way through the field from the 400m and travelled up behind the leaders in the straight.

But the jockey's luck almost ran out at the 200m when Pajaro was stopped in his tracks before he was able to regather his momentum to beat Hawkesbury Gold Cup winner Amovatio.

"It was a terrific win," Snowden said.

"Gee, if he had got beat you would be disappointed because he got stood on his head at the furlong."

Pajaro finished down the course behind Amovatio at Hawkesbury but Snowden said it wasn't hard to find an excuse for the five-year-old.

"We drew barrier one (at Hawkesbury) and tried to be a little bit more positive on him," Snowden said.

"The track was a bit iffy where he was and it really took it out of him.

"We were confident today getting him back on a firmer track that he would definitely run better but the barrier draw threw us a bit.

"Then when were going through the race ... we noticed so much speed with six or seven leaders. We thought we might be able to tuck into a spot and ride for luck. It panned out perfectly."

In a blanket finish where two lengths separated the first 10 horses across the finishing line, Pajaro ($21) beat Amovatio ($8) by a long head with Malice ($10) a short head away third.

Scone is Snowden's home town and Friday's success was his third in the Cup.

He won the race in 2011 with Dysphonia and in 2012 with Raspberries as the head trainer for Sheikh Mohammed's Australian racing operation.