Santos won the Madeira Islands Open to become the only the second Portuguese player to win on the circuit. The first was Daniel Silva 20 years ago.
"When you look at some of the players who have won the award in the past it's a real privilege to see my name next to theirs on the trophy," he said.
"It's been an amazing season and to end it be winning the award is more than I could have dreamed of.
"The goal for 2013 is to win again on the European Tour and to play my first Major. This award has given me the confidence to go and achieve my goals.
"Although you only have one chance to win the Rookie of the Year, hopefully I can win many more titles in the future."
Previous winners include Tony Jacklin, Nick Faldo, Sandy Lyle, Jose Maria Olazabal, Colin Montgomerie, Sergio Garcia, Ian Poulter and Martin Kaymer.