MORE: How it happened - Australia v South Africa
Keen to bounce back from a series-opening loss to the hosts on Friday, the South Africans were sent into the field by George Bailey, who was skippering the Australian side after Michael Clarke was ruled out of the series with a hamstring injury.
Career best figures from man-of-the-match Morkel (5/21) and an effective cameo from Dayle Steyn (3/35) saw Australia bowled out for just 154 in what was a disappointing innings from the hosts.
While some inspired bowling from Josh Hazlewood (5/31) gave Australia a chance, it was a case of having simply too few runs on the board as captain AB De Villiers (48) steered his side to victory.
The best-of-five series is now evenly poised at one win apiece, with the two sides set to face off again in Canberra on Wednesay.
What looked like a good batting wicket at the WACA couldn't help the Australian top order as David Warner fell in the first over, gloving a vicious ball from Morkel to wicketkeeper Quinton De Kock to depart for a duck.
Things didn't get better for the Australians from there, with Steyn sending Aaron Finch on his way for just eight after he looped one to Morkel at mid-on.
In trouble at 2-14, Australia needed a partneship but they didn't get it as Shane Watson (11) and Steve Smith (10) both failed to muster a meaningful challenge.
Playing in front of his home crowd, Mitchell Marsh gave the Australian scorecard some respectability as he battled away with Bailey for a fourth wicket partneship of 58 before the Australian captain fell to Vernon Philander for 25.
Matthew Wade did his best to continue were Bailey left off as he notched up 19 before becoming Morkel's third victim, caught behind by De Kock.
Morkel was at it again just two balls later as Glenn Maxwell chopped a short one back onto his stumps for a duck.
With Marsh running out of partners, the young batsman went on the offensive, eventually holing out to the bowling of Steyn for a brave 67 to bring Australia's innings to a close.
Chasing just 154 for victory, the Proteas knew time was on their side as they began their run chase.
They got off to a nervy start when De Kock departed for just 4 runs, brilliantly caught by Watson in the slips off the bowling of Hazlewood in the second over.
Hashim Amla, playing in his 100th ODI, didn't fare much better as he was sent packing by Johnson, edging one to Wade after failing to deal with a short ball.
That left the Proteas on 2-21 from seven overs, but unlike Australia before them, they had batsman to steady the ship as Rilee Rossouw and Faf Du Plessis went to work.
The pair put on 43 for the third wicket, wearing out the Australian attack with Rossouw eventually falling to Maxwell for 30.
That bought AB de Villiers to the crease, and from there it was essentially South Africa's game to lose.
The recently crowned ODI Player of the Year went on the offensive from the outset, cashing in on Johnson in particular as he put his side firmly in the driver's seat.
By the time he departed for 48, caught behind by Wade after inexplicably coming down the wicket to Hazlewood, South Africa were 6-141 and seemingly cruising to an easy win.
Two wickets in as many balls from Hazlewood made things interesting but some sensible stroke-play from David Miller (22) and a no-nonsense boundary from Steyn bought an end to any hope of an unlikely Australian win as South Africa finished on 7-157 to ease to a three wicket victory with 134 balls to spare.
Keen to bounce back from a series-opening loss to the hosts on Friday, the South Africans were sent into the field by George Bailey, who was skippering the Australian side after Michael Clarke was ruled out of the series with a hamstring injury.
Career best figures from man-of-the-match Morkel (5/21) and an effective cameo from Dayle Steyn (3/35) saw Australia bowled out for just 154 in what was a disappointing innings from the hosts.
While some inspired bowling from Josh Hazlewood (5/31) gave Australia a chance, it was a case of having simply too few runs on the board as captain AB De Villiers (48) steered his side to victory.
The best-of-five series is now evenly poised at one win apiece, with the two sides set to face off again in Canberra on Wednesay.
What looked like a good batting wicket at the WACA couldn't help the Australian top order as David Warner fell in the first over, gloving a vicious ball from Morkel to wicketkeeper Quinton De Kock to depart for a duck.
Things didn't get better for the Australians from there, with Steyn sending Aaron Finch on his way for just eight after he looped one to Morkel at mid-on.
In trouble at 2-14, Australia needed a partneship but they didn't get it as Shane Watson (11) and Steve Smith (10) both failed to muster a meaningful challenge.
Playing in front of his home crowd, Mitchell Marsh gave the Australian scorecard some respectability as he battled away with Bailey for a fourth wicket partneship of 58 before the Australian captain fell to Vernon Philander for 25.
Matthew Wade did his best to continue were Bailey left off as he notched up 19 before becoming Morkel's third victim, caught behind by De Kock.
Morkel was at it again just two balls later as Glenn Maxwell chopped a short one back onto his stumps for a duck.
With Marsh running out of partners, the young batsman went on the offensive, eventually holing out to the bowling of Steyn for a brave 67 to bring Australia's innings to a close.
Chasing just 154 for victory, the Proteas knew time was on their side as they began their run chase.
They got off to a nervy start when De Kock departed for just 4 runs, brilliantly caught by Watson in the slips off the bowling of Hazlewood in the second over.
Hashim Amla, playing in his 100th ODI, didn't fare much better as he was sent packing by Johnson, edging one to Wade after failing to deal with a short ball.
That left the Proteas on 2-21 from seven overs, but unlike Australia before them, they had batsman to steady the ship as Rilee Rossouw and Faf Du Plessis went to work.
The pair put on 43 for the third wicket, wearing out the Australian attack with Rossouw eventually falling to Maxwell for 30.
That bought AB de Villiers to the crease, and from there it was essentially South Africa's game to lose.
The recently crowned ODI Player of the Year went on the offensive from the outset, cashing in on Johnson in particular as he put his side firmly in the driver's seat.
By the time he departed for 48, caught behind by Wade after inexplicably coming down the wicket to Hazlewood, South Africa were 6-141 and seemingly cruising to an easy win.
Two wickets in as many balls from Hazlewood made things interesting but some sensible stroke-play from David Miller (22) and a no-nonsense boundary from Steyn bought an end to any hope of an unlikely Australian win as South Africa finished on 7-157 to ease to a three wicket victory with 134 balls to spare.