In the first round Morrison and Frangipanne De Toxandria went clear in 71.45s. A 63s time limit was set for the jump-off which Morrison won with a time of 50.33s.
Only 13 of the 19 qualifiers opted to come back for the jump-off with the others choosing to save their horses for the remainder of the week. Four of those went clear.
Kumeu's Lisa Coupe, a former two-time Lady Rider of the Year title winner, and Lotte were second in 51.83s. Waikato's Rachel Malcolm and Monte Carlo MVNZ were third with a time of 53.54s.
Julie Davey did the best of the Hawke's Bay starters with a fourth placing on Joligne De Carmel, the first of her two entries, which both qualified for the jump-off, with a time of 55.73s.
Davey, the 1997 and 1998 winner of the Lady Rider title, also qualified for the jump-off on Ngahiwi Stone but had eight faults in their second outing.
Waikato's Todd Magner had the fastest time in the jump-off of 50.28s on his thoroughbred Clydesdale-cross Awatuna Jonesy but a rail knocked down relegated him to fifth place and the fastest of the four faulters
Morrison, who took up showjumping in 2013, is competing at her fifth Horse of the Year. She didn't compete last year as she was Australia-based with a team of showjumpers.
"This is my first Horse of the Year class win. I have had lots of seconds and I really want that Lady Rider of the Year title," she said referring to Thursday's feature showjumping event.
"That's the only class I entered apart from this one."
The fact Frangipanne De Toxandria had two embryo foals while she was on the injured list added to the significance of today's title.
"We thought she was out for a good. She has been a mum and come back," Morrison added.
The wind created havoc for course attendants throughout the event as they dealt with fallen jumps and flying umbrellas.
Hawke's Bay's Simon Wilson, who tasted Olympic Cup glory in 2004, was among those who opted out of the jump-off after going clear in the first round on McMillans Ariados.
His was the third of seven consecutive clears, a tremendous feat considering the conditions.
Hawke's Bay's Melody Matheson and Cortaflex Graffiti MH finished their jump-off round in 52.67s and with four faults.
Te Awamutu's Emily Hayward, who won the Olympic Cup and a second consecutive Young Rider title last year, didn't have a memorable start to this year's show. Riding her 10-year-old gelding Belischi HM, last year's successful Olympic Cup combination, Hayward, was eliminated in the first round after two refusals.
Wednesday's schedule:
8.30am: Horse 1.35m.
11:15am: Six Year Old Horse of the year Championship.
1:30pm: Wade Equine Coaches Amateur Rider Final 1.10m–1.20m.
4pm: Norwood Gold Cup 1.45m.