With Johnson ripping through their batting line-up, England was bowled out for a paltry 172 in reply to Australia's first innings of 9(dec)-570 and now batting a second time, the home side is 3-132 with an overall lead of 530 with two days to play on a flat Adelaide Oval deck.
Australian captain Michael Clarke decided to bat again to give his bowlers some rest before England's second innings and then saw his team slump to 2-4 with Chris Rogers out for two and Shane Watson for a duck.
Clarke and David Warner then steadied things for the Australians before Clarke was bowled by a superb delivery from Monty Panesar for 22.
However, at stumps on Day 3 now Warner remains 83 not out with Steve Smith 23 and Australia 3-132 to be 530 runs ahead of England.
Earlier, Johnson finished with figures of 7-40 from 17.2 overs as he once again struck fear into an England batting line-up that had no answer for his fiery left-arm fast bowling.
Aside from Bell's fighting not out 72 and opener Michael Carberry's 60, no England batsman showed a willingness to hang in for the fight on Day 3 with the visitors bowled out for a paltry 172 on a flat Adelaide Oval wicket.
After poor dismissals from bad attacking shots to Joe Root and Kevin Pietersen early in the day, England steadied somewhat thanks to Carberry and Bell, but once Carberry fell for 60 things fell apart and the visitors went from 3-111 to being all out for 172, losing 7-61.
That leaves England 398 runs behind Australia's first innings score of 9(dec)-570 set up by 148 from captain Michael Clarke and 118 from Brad Haddin.
Clarke decided not to enforce the follow-on, though, despite having the option to do so allowing his bowlers some time to rest after bowling 68.2 overs before having another crack at England's batsmen over the last two days looking to take a two-nil series lead heading to Perth on Friday.
After Australia piled on 570 in its first innings before declaring with just over 20 overs remaining on Day 2, England lost captain Alastair Cook before stumps with a beauty of a delivery from Johnson.
That meant England came into the third day on 1-35 with plenty of hard work, patience and restraint required to hang in there, and make Australia have to work hard for their wickets.
However, that message didn’t appear to get passed down to new No. 3 batsman Root.
Shortly after Australian off-spinner Nathan Lyon was brought on to bowl, Root attempted a slog sweep shot looking for easy runs and only managed to hit it up in the air for Chris Rogers to take a comfortable catch in the deep.
Root had been bogged down somewhat facing 80 deliveries for his 15 with just the one boundary, but his was a terribly applied shot in a time when restraint was required from the English batsmen.
The visitors were then 2-57 and shortly after 3-66 when Pietersen played an even worse shot to be out for four.
He had already survived a close caught behind appeal that was struck down, but shortly after sauntered down the pitch and tried to clip Peter Siddle in the air through mid-wicket. He only managed to hit it straight to George Bailey, though, who took a juggling catch.
Bell came to the crease then for England and immediately took the attack to Australia and hit Lyon out of the attack and was scoring at better than a run a ball for some time, but he soon lost his partner at the other end.
Carberry was looking good particularly when playing strokes through the off-side field and made good connection on a pull shot off Shane Watson just before lunch, but David Warner pulled off a spectacular one-handed catch to dismiss him for a well-made 60.
England went into lunch at 4-116 and just one more run was added after the break before debutant Ben Stokes was trapped in front lbw to Johnson for one.
Four balls later Matt Prior's dismal form against Australia both in the series in England and now the current one continued when he made a four-ball duck edging Johnson behind to wicket-keeper Haddin.
The very next ball, after a long delay with Stuart Broad wanting a shining metal bolt on the sight screen taken care of, Johnson took out Broad's leg stump as he jumped across the crease to be on a hat-trick.
Johnson missed the hat-trick but it took him only two more overs before he got rid of Graeme Swann for seven when he slashed at a wide one to edge it to Clarke in second slip.
The very next delivery again Johnson bowled a full and fast one that James Anderson had no answer for, and after he bowled him Johnson gave his rival quick a big stare down.
Again he missed his hat-trick and Bell continued to fight hard making 72 with Monty Panesar sticking with him before Johnson returned to the crease and clean bowled Panesar for two from 35 balls to end England's innings at 172, 398 behind Australia.
AUSTRALIA FIRST INNINGS 9(dec)-570
ENGLAND FIRST INNINGS
A COOK b Johnson 3 (11)
M CARBERRY c Warner b Watson 60 (144)
J ROOT c Rogers b Lyon 15 (80)
K PIETERSEN c Bailey b Siddle 4 (12)
I BELL not out 72 (106)
B STOKES lbw Johnson 1 (12)
M PRIOR c Haddin b Johnson 0 (4)
S BROAD b Johnson 0 (1)
G SWANN c Clarke b Johnson 7 (7)
J ANDERSON b Johnson 0 (1)
M PANESAR b Johnson 2 (35)
Sundries (3lb 2w 3nb) 8
Fall: 9 (Cook), 57 (Root), 66 (Pietersen), 111 (Carberry), 117 (Stokes), 117 (Prior), 117 (Broad), 135 (Swann), 135 (Anderson), 172 (Panesar).
Bowling: M Johnson 17.2-8-40-7 (1w 2nb), R Harris 14-8-31-0, N Lyon 20-5-64-1, P Siddle 14-4-34-1 (1w 1nb), S Watson 3-3-0-1.
Batting time: 315 mins. Overs: 68.2.
AUSTRALIA SECOND INNINGS
C ROGERS c Prior b Anderson 2 (10)
D WARNER not out 83 (117)
S WATSON c Carberry b Anderson 0 (2)
M CLARKE b Panesar 22 (51)
S SMITH not out 23 (54)
Sundries (1b 1lb) 2
Three wickets for 132
Fall: 4 (Rogers), 4 (Watson), 65 (Clarke).
Bowling: J Anderson 7-1-19-2, S Broad 6-0-19-0, G Swann 9-3-31-0, B Stokes 7-3-20-0, M Panesar 10-0-41-1.
Batting time: 164 mins. Overs: 39.
Umpires: Marais Erasmus (RSA), Kumar Dharmasena (SRL).