Burns, the only Australian player in the top five, took home the Johnny Warren Medal, receiving 577 votes from his playing peers ahead of Adelaide United playmaker Marcelo Carrusca (366 votes), Melbourne Victory's Fahid Ben Khalfallah (307 votes) and Kosta Barbarouses (277 votes).
Reds' Sergio Cirio (245 points) rounded out the top five.
"There's so many good players in the A-League now it's really hard to think you're up there with the best," a surprised Burns said.
"I've still got to pinch myself.
"It's the biggest award of the year and on a personal level it's fantastic.
"I actually thought Ben Khalfallah was going to win so when I saw his name called third I was wondering who was going to win.
"I don't how I got over the line."
Burns first burst on to the A-League scene with Adelaide United in 2006 before heading abroad with stints in Europe and Asia.
He returned home to join the Newcastle Jets in 2013 but it was with the Phoenix this season that the 27-year-old frontman really made a name for himself.
He netted an impressive 13 goals and earned a place in the Socceroos' squad, playing a key role in their triumphant Asian Cup campaign.
"It was definitely a drive to come back and get back in the Socceroos," Burns said.
"That was the whole incentive in coming back to the A-League. To get back and start playing well.
"So to be called up for the Socceroos was a great honour and to be involved in the Asian Cup."
Burns credited Phoenix mentor Ernie Merrick for his form.
He said the attacking style Merrick implements, which had Wellington looking like title contenders before falling away to finish fourth on the ladder, brought the best out in him.
"The Wellington Phoenix system that I was playing in under Ernie Merrick - he really got the best out of my performance, he knew how to change me as a player and make me more attacking.
"So I think that's been the difference to the previous years."
Sydney FC's Austrian marquee player, Marc Janko, took home the Golden Boot award with his 16 strikes making him the league's top goal scorer this season while Melbourne Victory's premiership-winning coach Kevin Muscat was named A-League Coach of the Year ahead of Sunday's grand final show down against the Sky Blues.
In other awards Socceroo shotstopper Eugene Galekovic collected the A-League Goalkeeper of the Year Award for a record fourth time while Adelaide's James Jeggo was named the Young Footballer of the Year.
Adelaide United defender Tarek Elrich's superb solo effort against Melbourne City FC in the final round of the regular season was voted the A-League Goal of the Year.
Meanwhile, Jarred Gillett was named the Referee of the Year award for the second time.
