The world No 5 and 2009 US Open champion, edged out Barcelona superstar Messi, who scored 46 La Liga goals last season, at the Sporto Argentino Festival.
'The Tower of Tandil' won four titles this year and was runner-up at the Indian Wells and Shanghai Masters.
He also made the semi-finals at Wimbledon, losing a five-set epic to Novak Djokovic in the longest men's last-four match in the history of the tournament.
"I am very happy to have received the Gold Prize of Clarin," del Potro wrote on his Facebook page.
"It was a great year, much better than I expected. I was there, fighting in the first place. The main thing is I feel very close to the top of the world again. I'm already looking at next season."
Outside of the "Big Four" - Roger Federer, Rafael Nadal, Novak Djokovic and Andy Murray - Del Potro is the only other man to have won a Grand Slam since 2006.