Gilchrist claimed three sixes in his swashbuckling unbeaten knock of 67 to reach his century of sixes as the Australians powered to 542 for five declared after last week's declaration of 551 for four in Brisbane.
Skipper Ricky Ponting called a halt and flung the new ball to his fast bowlers Brett Lee and Mitchell Johnson to ram home the advantage, only to miss out on a breakthrough.
Openers Marvan Atapattu (18) and Michael Vandort (12) survived 12 overs before bad light ended play for the day with the tourists on 30 without loss.
Gilchrist reached an unprecedented 100 Test sixes with panache by hoisting Muttiah Muralitharan for consecutive sixes.
The explosive-hitting wicketkeeper, this week voted Australia's greatest one-day cricketer, twice smacked Muralitharan over mid-wicket, the last one clearing the ground's perimeter fencing and forcing match officials to find a replacement ball.
On Andrew Symonds reaching his fourth half-century in his 15th Test match, Ponting declared the innings six overs after tea and chased to capitalise with early Sri Lankan wickets before being thwarted by fading light.
It was a torrid day in the field for the beleaguered Sri Lankans, toiling away with only three bowlers for most of the time after paceman Farveez Maharoof failed to play with a foot injury.
The Australians backed up their match-winning innings in last week's Brisbane Test canter with another day of batting carnage.
Symonds and Gilchrist took to the Sri Lankan bowling after Phil Jaques (150) and Michael Hussey (132) plundered centuries.
Gilchrist breezed to an unbeaten 67 off 77 balls with seven boundaries and three sixes and Symonds 50 off 71 balls with four fours and a six. They sailed along in an unbroken 95-run partnership off 125 balls.
Australia's domination and subsequent declaration almost certainly spelt the end of Muralitharan's quest for six more wickets to break Shane Warne's world record of 708 wickets, symbolically in Warne's backyard.
It is the final match of the two-Test series and with Sri Lanka's batsmen under the pump the spinner is unlikely to get a bowl again in the Hobart Test.
The Sri Lankans were buried by an innings and 40 runs in last week's first Test and have so far showed no discernible sign of improvement in Hobart.
Maharoof's injury heaped extra pressure and workload on the Sri Lankan bowlers with Malinga finishing with 1-156 off 35 overs, Dilhara Fernando 2-131 off 26 overs and Muralitharan 1-140 from 46 overs.
The remarkable Hussey nudged his Test average to 84.63 before he fell leg before wicket to Fernando for 132.
Hussey ranks second only to Don Bradman (99.94) with the highest Test average from a minimum of 20 innings.
It was the 32-year-old left hander's seventh century in 28 Test innings and once again underlined his immense value to the Australian top order.
Hussey batted for 282 minutes and hit 18 boundaries and a six over mid-wicket off Muralitharan.
He put on 125 runs for the fourth wicket with Michael Clarke, who later fell to an acrobatic catch by wicketkeeper Prasanna Jayawardene down the leg-side off Malinga for 71.
Clarke, who had an unconquered 145 in the Brisbane Test, was at the crease for close to three hours and hit eight boundaries.