Horwill polled 55 per cent of the vote in the rugby.com.au poll, 26 per cent more than his nearest challenger.
Star scrum-half Will Genia finished second with 29 per cent, with the four other nominees receiving minimal backing.
Brumbies back rower Ben Mowen and Rebels utility back James O'Connor were tied on 6% of the votes, while the club captains at the Waratahs and Force, Dave Dennis and Matt Hodgson, both ended up with just 2%.
Horwill was named his country's captain prior to the 2011 World Cup but has endured a frustrating year in the run up to the Lions tour.
The 27-year-old hasn't worn Wallaby colours since the end-of-season tour in 2011, with a serious hamstring problem preventing him from playing in every Test in 2012.
He finally returned to Super XV action late last month after minor ankle damage prolonged his absence and, despite his lack of recent international action, is a near certainty to start against Warren Gatland's troops if he stays fit.
Horwill currently has 35 Test caps to his name and led the Wallabies to their first Tri Nations crown in a decade on his debut as skipper against the All Blacks in August 2011.
He also guided the Reds to the Super Rugby title the same year and has led Australia to six wins in his eight Tests as captain.
Deans selected four skippers in 2012 as injuries decimated his squad but two of those are unavailable this time around.
David Pocock took over from Horwill for the summer Tests against Scotland and Wales but was injured in the opening Rugby Championship loss to New Zealand and has since been ruled out of the Lions series with ACL damage.
Genia then took on the mantle prior to suffering a serious knee injury against South Africa, with Nathan Sharpe picking up the baton for the final few games of his career before retiring after the win over Wales in December.