Ben Thompson has denied his good mate Beau Mertens in a close finish to the Rising Stars Final for apprentices at Flemington.

But Mertens' second placing on Khutulun was still enough for him to clinch the overall series win.

Saturday's Rising Stars Final over 1800m was the culmination of a 21-race series in Victoria for junior riders during the 2015-16 season.

Apprentices earned points based on finishing positions of their horses in the respective races.

Thompson's mount, Savannah Moon, rallied to beat Khutulun by a neck in Saturday's fillies and mares handicap after Khutulun loomed strongly under Mertens inside the final 200m.

Thompson earned 12 points for his win on the Rod Symons-trained Savannah Moon to finish fourth in the series.

Brandon Stockdale was the only apprentice capable of beating Mertens on points if he had won on Melaleuca, but the mare finished sixth.

Thompson, who brought up a winning double at the meeting, said it was nice to win against his fellow apprentices.

"It's pretty competitive between the bunch," Thompson said.

"I don't know where I was in order of the points but hopefully it puts me up there and it was just nice to get the one that matters, I guess."

Thompson and Mertens started together with Cranbourne trainer Mick Kent.

While Mertens remains with Kent, Thompson is now with the Alan Williams stable at Cranbourne.

"We're pretty close," Thompson said.

"We both sort of came through together. We had our first jump-out on the same day, first official trial on the same day and I think our first race rides were a month apart."

Mertens, who turned 19 on Friday, would have loved to have capped the series with victory on Saturday but was still pleased to clinch the series.

"(Khutulun) loomed up at the 200-metre mark like she was going to put them away quite easily, but she's only got a short sprint on her," he said.

"I finished fourth in the series last year and ever since then I made it a goal to finish closer and even try to win it this year.

"It's worked out really well for me in the end."