Despite winning Saturday's race which was restricted to apprentice riders only, Nugent finished second in the Rising Stars Series which comprises more than 20 apprentices-only races around Victoria during the season in which the riders earn points for top-five finishes.
Nugent earned 12 points for his win on El Questro in the Final but Campbell Rawiller had gone into the event with an unassailable 16-point lead.
Rawiller finished second aboard the Grahame Begg-trained Beauty Bolt in Saturday's race, notching another six points to finish 10 ahead of Nugent in the overall points standings.
Rawiller, son of prominent Sydney jockey Nash Rawiller, won four of the heats during the Rising Stars Series in his first season of race riding.
"It's been a competitive series all season, really," Nugent said.
"We've been running second for quite a long time and it's good to pinch a winner. I understand that it is Allison's first winner here at headquarters so even more special."
El Questro had finished second twice last winter at Flemington, including a narrow defeat in the Leilani Series Final and in the corresponding race to Saturday's, then had an extended break after that preparation.
In her fourth Flemington appearance of this campaign, El Questro ($6) strode clear in the straight in the 1400m benchmark-90 event for fillies and mares to score by three lengths, with Beauty Bolt ($5.50) running home into second.
Sheehan bred and also part-owns El Questro who took her overall record to five wins from 25 starts.
"She pulled up a bit distressed and out of sorts post race last time (after Leilani Series Final)," Sheehan said.
"We were really worried but she bounced back quickly and I couldn't find a reason not to come here today.
"We've ticked all the boxes this week and I'm just really happy."