Australian opener Marsh made 78 and added 135 with captain Ricky Ponting (64) as they made 249-9 from their 50 overs, with Makhaya Ntini taking 3-39 for South Africa in their second one-day international at the MCG on Sunday. Jacques Kallis (72) and AB de Villiers (44) then put the tourists in charge.
But a mini-collapse from 145-2 to 172-5 led to a slump in the run rate and, needing 17 from the last over, they finished five runs adrift on 244-6.
Ponting was delighted by the victory but afterwards admitted he had got the timing of Australia's batting powerplay wrong. They did not take it until the start of the 40th over, but Ponting said he should have used around the 15-over mark when he and Marsh were well-set.
"[Dale] Steyn and Ntini had both bowled six overs at that stage. If we'd took it then, it would have forced them to bring those guys back and they would have been short at the back end," he commented.
"It's one of those rules you have to be very flexible with and try to use it to your advantage every time - and today we didn't use it as best as we could have."
David Warner made his one-day international debut for Australia in place of the injured Michael Clarke, but he managed only five before edging a ball from Steyn to keeper Mark Boucher. Proteas paceman Ntini got a couple to whizz past Ponting's helmet, but the Australian captain responded with some adventurous hitting - although he needed two slices of luck when he was dropped by Neil McKenzie on 10, and Ntini just after he had reached 50. Marsh was also dropped just after reaching his fifth half century in 10 matches, with stand-in skipper Johan Botha the culprit, but he and Ponting eventually fell in quick succession.
Ponting holed out to De Villiers at deep backward square leg, while Marsh was superbly caught by Kallis at extra cover off JP Duminy's occasional off-spin.
At that stage, Australia were 166-3 with 17 overs remaining and the Hussey brothers at the crease, and when the powerplay was finally taken the first ball saw Mike Hussey (28) spoon Kallis to Herschelle Gibbs at backward point.
Cameron White fell cheaply and David Hussey, Brad Haddin, James Hopes and Ryan Harris - making his ODI debut in place of Shaun Tait - hit just two boundaries between them as they got bogged down in the final overs.
South Africa lost Hashim Amla cheaply at the start of their reply and Gibbs was caught on the mid-wicket boundary for 19 when he tried to hit Hopes over the top. But with Kallis and De Villiers adding 93 for the third wicket, the visitors must have been optimistic of forging a 2-0 lead in the series.
As with Marsh and Ponting, however, both fell in quick succession to derail the South African reply. Honours are now even going into Friday's third ODI in Sydney.
"I don't think we can be too disappointed. Both sides could be 2-0 up at this stage, it has been that close," said Botha. "It is probably a fair reflection at the moment that the teams are locked at 1-1 and there is everything to play for in the three remaining fixtures."

===========================================
Australia Innings
===========================================
Marsh c Gibbs b Duminy                   78
Warner c Boucher b Steyn                  5
Ponting c de Villiers b Kallis           64
M Hussey c Gibbs b Kallis                28
D Hussey c A Morkel b Ntini              19
White c Botha b Steyn                     1
Haddin run out                           23
Hopes c A Morkel b Ntini                  8
Harris c Duminy b Ntini                   7
Bracken not out                           0
Extras: (8w 8lb)                         16
===========================================
Total: (for 9  wkts, 50 overs)          249
===========================================

Bowling: Steyn 10.0 2 36 2, Ntini 9.0 0 39 3, Kallis 10.0 0 57 2, A Morkel 8.0 0 46 0, Botha 7.0 0 40 0, Duminy 6.0 0 23 1

===========================================
South Africa innings
===========================================
Gibbs c M Hussey b Hopes                 19
Amla c White b Hilfenhaus                 8
Kallis c D Hussey b Hilfenhaus           72
de Villiers run out                      44
Duminy run out                           35
McKenzie b Harris                         8
Boucher not out                          37
A Morkel not out                         11
Extras: (5w 3b 2lb)                      10
===========================================
Total: (for 6 wkts, 50.0 overs)         244
===========================================

Bowling: Hilfenhaus 10.0 2 60 2, Bracken 10.0 0 38 0, Harris 10.0 0 54 1, Hopes 10.0 0 43 1, D Hussey 7.0 0 28 0, White 3.0 0 16 0
Toss: South Africa, who chose to field first
Series: 5-match series level 1-1
Player of the match: S Marsh (Australia)
Umpires: I Gould and R Tucker
TV umpire: P Reiffel
Match referee: R Madugalle (Sri Lanka)