The 23-year-old flanker topped the RUWC poll ahead of New Zealand's World Cup-winning coach Graham Henry, France captain Thierry Dusautoir and Wales wing Shane Williams, who has retired from Test rugby.
Warburton was the youngest captain at the Rugby World Cup and he led Wales with distinction to their best finish since 1987.
The tournament ended in personal disappointment but Warburton was widely applauded for his dignified response to being sent off in the semi-final defeat to France.
RUWC chairman Paul Morgan said: "Sam has had an exemplary year, leading Wales with great dignity, marking himself out as one of the leading candidates to captain the Lions in 2013.
"He's a worthy recipient of the Pat Marshall Trophy, just beating Graham Henry in a poll of rugby media. He joins an illustrious list of winners."
The RUWC presented their special award to former Wales international Richard Parks, who completed the remarkable feat of climbing the highest peak on each of the seven continents and hiking to both poles within seven months.
Parks embarked on the challenge with the aim of raising £1million for Marie Curie Cancer Care.