Johnson was left stranded on 92 as he ran out of partners to aid his century quest with the early departure of tailenders Nathan Lyon and Jackson Bird in quick succession on the third day.
The big smiling left-arm veteran was duly named man-of-the-match in another fairytale chapter in his Test comeback.
Sri Lanka was all-out for 103 in their second innings after just 156 in the first time at bat and Australia won by a whopping innings and 201 runs.
Match scores were Sri Lanka 156 and 103, to Australia's 460, after the visitors won the toss and batted first.
The tourists had three batsmen unable to take their place at the crease and Sri Lanka's innings finished just after drinks on the third day at the half-way stage of the scheduled five-day clash.
Johnson, 31, was the destroyer as Sri Lanka lasted a measly 24.2 overs after batting for only 43.4 overs in their pathetic first innings.
The firebrand quick inflicted ferocious physical and wicket-smashing pain on the hapless tourists with crucial first-over breakthroughs with a spectacular run-out of Sri Lanka opener Dilshan Karunaratne at the bowlers end and a wicket next ball.
Johnson wrapped stinging fiery deliveries into the gloves of champion Sri Lankan batting great Kumar Sangakkara and tailender Dhammika Prasad.
Wicketkeeper Prasanna Jayawardene was also not able to bat with a broken finger he copped from a Johnson fireball in the first innings.
Johnson wreaked havoc through Sri Lanka's disastrous innings when he sent star batsman Sangakkara out of action with a possible broken left index finger early after lunch.
Johnson skittled the dishevelled tourists as the big left-armer continued a stunning return to the Test arena after just one appearance with the Australian team in Perth four weeks ago coming back from a year in the wilderness in injury recovery.
Sangakkara departed on 27 and left all-rounder Angelo Mathews followed quickly after for an innings top-score 35.
Johnson finished with 2-16 from eight lively overs to add to his first innings 4-63, Bird collected debut match figures of 4-61 with his 2-29 in the second innings as Australia's main destroyers.
Australia's high powered pace battery performance tends to reinforce the contentious rotation system with Johnson so fresh and vibrant and Bird a unabashed success on debut.
Australia was dismissed for 460 early into the morning session when Johnson was left painfully short of his second Test ton as the home side led on the first innings by 304.
Sangakkara, who brought up his 10,000th Test runs in Sri Lanka's first innings debacle, retired hurt for urgent attention to a severely swollen finger and is serious doubt for any further action in this disaster and probably to miss the third clash of the series in Sydney.
Bird continued his impressive debut when he chimed in with the sensational dismissal of Sri Lanka captain Mahela Jayawardene in the second over and then trapped Thilan Samaraweera flush in front leg-before-wicket.
Bird, 26, had 2-10 from his five-over second innings spell after he collected 2-32 from 13 overs in his first outing as Australia's newest paceman.
The accurate seamer could have had even better figures if big Shane Watson had pouched a sharp chance in the gully during the first over after lunch.
Watson, nursing a strained left calf, muffed a right-handed attempt to snatch Mathews as he cut a short and lifting Bird delivery with the addition of just two runs from the luncheon total.
The visitors lost wickets on the third and fourth balls of Johnon's opening over and then the last ball of Bird's first of his spell.
Inside six overs the bungling tourists were 4-13 and tumbling toward a defeat inside three days and a series-winning 2-nil lead to the home side.
Australia's barnstorming bowling and stifling fielding performance seriously threatened to end Melbourne's Boxing Day traditions inside the third day and not even get into the weekend.
Jayawardene attempted to let the Bird outswinger go but chopped his bungled defensive effort onto his stumps from the final ball of the second over of the dishevelled start.
Johnson sent Hobart century-maker Tilakaratne Dilshan packing with a sharp lifting ball into his ribs and a popped catch to Ed Cowan at short-leg on just the fourth ball of the innings.
Seamers Shaminda Eranga and Dhammika Prasad took three Aussie wickets each and Mathews two for Sri Lanka.
It is the second time in his 49 Tests that Johnson has been left stranded in the 90s.
Australia resumed on Friday at 8-440, with Johnson on 73 and Lyon without a score.
Johnson snatched four Sri Lankan scalps on the opening day of the Melbourne Test to become the 14th Australian bowler with 200 wickets at the game's elite level.
He is playing only his second Test in a little over a year when he suffered a career-threatening foot injury in South Africa late into 2011 and rebuilding his standing as a potentially permanent member of the Australian side.
He was forced to reclaim a spot in Australia's bowling contingent through the contentious rotation system after menacing performances at interstate first-class level with Western Australia.
Johnson snatched 17 Sheffield Shield wickets at an average of 29 in five first-class outings with his adopted state, where it was more his venomous pace in intimidating bounce that appealed to selectors for his recall to the expanding Aussie pace brigade.
Johnson scored his only Test century, an unbeaten 123 against South Africa at Cape Town in March of 2009 in the same three-match series that the gritty left-hander remained 96 not out in Johannesburg.