Roma captain Totti wins Golden Boot
However, the Dutchman ended his campaign with 25 goals, having been substituted at half-time against Real Mallorca.
The contest is decided via a coefficient system based on the difficulty of scoring in each nation.
Afonso Alves came in third after scoring 34 goals for Dutch outfit Heerenveen.
In terms of the system, Totti earned 52 points, whereas van Nistelrooy's 25 goals were worth 50 points.