The visitors went in to the game without a win in eight pre-season games, their plight highlighted when former Killie striker Colin Nish missed a first-half sitter.
The Easter Road club probably thought they had done enough to earn a point but with the game heading for a draw, Hamill, on five minutes earlier for Simon Ford, drove a David Fernandez pass into the corner of the net from 25 yards out.
Before a ball had been kicked this season, Hibs boss Mixu Paatelainen found himself under pressure.
Whispers of dressing discontent at Easter Road had grown in volume in the build-up to the new season and although the visitors looked purposeful at times, this result will simply add to his woes.
Killie seemed out of sorts early on and the erratic-looking debutant Manuel Pascali was booked in the fifth minute for a clumsy foul on David van Zanten..
In the 16th minute Nish had an easy chance to open the scoring after Steven Fletcher had robbed Hay but the former Killie striker trundled his shot from 16 yards straight at Alan Combe.
Moments later, Combe made a fine save from Fletcher after the Scotland striker had turned Killie defender Ford 10 yards from goal with a clever flick.
The game swung from end to end with plenty of crunching tackles to keep the crowd animated but Killie were dealt a blow when defender Ryan O'Leary had to be replaced by Frazer Wright, following a clash with Nish.
Slowly Kilmarnock began to work themselves into the game and Garry Hay's fine cross from wide on the left found no takers but Hibs remained a threat on the counter.
In the 31st minute Killie's talented playmaker Mehdi Taouil showed himself for the first time in the game when he picked up a Jamie Fowler pass, skipped past Hibs defender Chris Hogg and fired in a tremendous right-footed drive from 30 yards which visiting keeper Andy McNeil did well to tip over the bar.
Kilmarnock finished the half strongly but just before the break Combe was in a good position to deal with a decent shot from Hibs substitute Ross Chisholm, who had replaced the injured Steven Thicot just after the half-hour mark.
The second half continued in an open fashion with both sides showing intent to go for the win, albeit with little finesse on show.
In the 54th minute, after Pascali had brought down Dean Shiels on the edge of the box to concede a free-kick, Fletcher curled his shot harmlessly over the bar.
At the other end, from a Taouil corner, Keenan cleared Wright's header off the line seconds before Paul Hanlon fired over Combe's bar with a powerful drive from 25 yards.
On the hour mark, Filipe Morais replaced the tiring O'Brien but three minutes later it was Nish, standing in a packed Killie six-yard box, who unintentionally blocked skipper Rob Jones' goal-bound header from a Shiels corner.
In the 67th minute Killie midfielder Craig Bryson broke away from Shiels, took a few steps and hammered a 35-yard drive inches over.
Occasional chances came along at both ends.
In the 73rd minute Combe pulled another fine save from Morais, beating away a powerful 20-yard drive, and moments later McNeil had to rush from his goal to block a close-range drive from Danny Invincibile.
But in the 80th minute Hamill picked up a Fernandez pass 25 yards from goal and drove a low shot past McNeil and into the corner of the net.
Four minutes of injury-time were added and, with Hibs piling forward, Invincibile wasted a couple of half-chances to increase the home side's lead.