Madison Crowe on Brogan was just behind them with 37.8 penalties and Woods followed on her second ride, Defies Logic, with 38.3 penalties.
The showjumping phase saw Woods take the lead with Defies Logic, after one of only two clear rounds.
Meanwhile, LV Award dropped to second after having two rails down.
Crowe held third position despite having a rail down, while defending champion Tayla Mason moved into fourth place after posting the other clear round on Lucy with Diamonds.
On Sunday, Bing Allen's cross-country course proved a serious challenge for the young riders, with Woods not finishing on either of her horses, and Mason suffering a nasty fall.
Cantabrian Crowe posted a clear round inside the time, with Brogan, to take the title from Lauren Alexander on BMW Ripley, who posted the only other clear inside the time.
Fellow Cantabrian Bonnie Farrant was third on Kaipara Dior, adding four cross-country time penalties and four penalties for dropping a showjumping rail.
Collett and Mi Focus finished fourth after incurring 13.6 cross-country time penalties.