Mark McLaughlin scored a shock opener for the visitors at Parkhead after three minutes and in fact it was only Hoops keeper Fraser Forster who prevented the home side falling further behind with some impressive saves as the home side struggled to get going.
But in the 25th minute Maloney, back in Craig Levein's squad for the forthcoming Euro 2012 qualifying double-header against the Czech Republic and Spain, levelled with a header.
The former Aston Villa player put the Hoops ahead with a wonderful free-kick after the break before Gary Hooper sealed the win that takes them above Old Firm rivals Rangers on goal difference.
Neil Lennon's men went in to the game looking for their seventh successive SPL win of the season and knowing that victory over the Accies by two clear goals would take them above their Old Firm rivals, who had come from behind to beat Hearts at Tynecastle earlier in the day.
But there was a tremor among the Hoops fans when the visitors took the lead through McLaughlin.
Dougie Imrie's searching corner from the right was headed back across goal by the unmarked Martin Canning and his fellow defender bundled in from six yards out.
Moments later, with the home defence in disarray, Forster had to move quickly from his goal to make a fine save from Accies striker Nigel Hasselbaink, who had raced clear.
Forster was soon forced in to another two saves in quick succession, pushing Imrie's drive past the far post for a corner and then, from the set-piece, tipping Simon Mensing's header over the bar.
As Celtic worked their way back in to the game, striker Georgios Samaras, back in the side at the expense of Anthony Stokes, tested Hamilton keeper Tomas Cerny with a drive from the edge of the box.
Celtic had rid themselves of most of their early nerves to take control of the game and in the 25th minute Maloney grabbed the almost inevitable equaliser.
Ki Sung-Yueng's arching corner from the right was met by Parkhead stopper Daniel Majstorovic, who headed towards the packed six-yard box where the former Hoops youth player reacted first to head in.
It was now backs-to-the-wall defending for the Lanarkshire side as they tried to cope with wave upon wave of Celtic attacks.
But the New Douglas Park men held firm, albeit at times desperately, and minutes from the break Flavio Paixao flashed a shot over the bar from the edge of the box when he ought to have tested Forster, following more indecision in the Celtic defence.
There were again some signs of uncertainty in the Celtic defence at the start of the second half, which gave Hamilton some encouragement.
However, in the 50th minute, Hoops defender Glenn Loovens had a decent chance from Ki's corner but headed high over the bar, moments before Maloney had a drive from the edge of the box saved by Cerny.
The Parkhead side slowly turned the screw and the Accies were let off the hook by Majstorovic in the 58th minute when he headed a Ki corner over the bar.
There were howls from the home fans when Celtic again allowed Canning a free header from an Imrie corner but this time the ball was clutched under the bar by Forster.
But in the 64th minute jeers turned to cheers when Maloney fired the Hoops ahead with a wonderful free-kick.
Skipper Scott Brown had been bundled off the ball by James Goodwin and after some delay to allow Stokes to replace Efrain Juarez, the Scotland striker curled an unstoppable shot past Cerny and into the far corner.
In the 71st minute Hooper sealed the victory when he took advantage of slack play by Accies before rifling low past Cerny from the edge of the box.
Celtic were cruising and Samaras and Ki both had attempts on goal which failed to hit the target.
The home fans were looking for more goals and Cerny made a save at his near post from Maloney.