Jonathan Paget withdrew Bullet Proof before the cross country after the horse seemed a little sore.
Just 32 of the 50-strong field finished all three disciplines.
Nicholson's win - on the back of his victories in four star events at Burghley, Pau and Kentucky firmly reinforce his top ranking and strangle-hold of the HSBC FEI Classics Series.
The winner of the classics will pocket $US150,000.
Results -
1 Andrew Nicholson (NZL) Mr Cruise Control (owned by Nicola and Robin Salmon and Nicholson) 38
2 Zara Phillips (GBR) High Kingdom 39.7
3 William Fox-Pitt (GBR) Neuf des Coeurs 47.7
4 William Fox Pitt (GBR) Lionheart 48.2
5 Kevin McNab (AUS) Clifton Pinot 51.5
6 Andrew Nicholson (NZL) Rathmoyle King (owned by Gillian Morris-Adams, Carolyn Taylor and Carolyne Ryan-Bell) 56
8 Jonelle Richards (NZL) Flintstar (owned by Darnelle Hubbard, Tim Price and Mrs Grey) 59.5
Jonathan Paget (NZL) Bullet Proof (owned by Joseph and Alexander Giannamore) withdrawn before cross country, Andrew Nicholson (NZL) Rathmoyle King (owned by Gillian Morris-Adams, Carolyn Taylor and Carolyne Ryan-Bell) 48 14, Andrew Nicholson (NZL) Qwanza (owned by Rosemary and Mark Barlow) eliminated in cross country.