Australia won the second game by five wickets, restricting South Africa to 144 for nine in 50 overs and then recovering from 21 for three to sweep to success at 145 for five in 24.3 overs.
The opening day-night game in Durban on Wednesday went to South Africa by six wickets, and the final contest is in Johannesburg on Sunday.
Gilchrist was aided by tight bowling and loose batting as he beat the previous best of five victims in a one-dayer which was shared by 18 wicketkeepers who between them achieved it a total of 26 times.
South Africa's batsmen did themselves no favours by playing expansively against the polished Australian bowlers on a pitch of good bounce, with eight men falling to close catches.
Glenn McGrath was in miserly form, taking two for 13 in 10 immaculate overs, while fellow paceman Brett Lee was the top wicket-taker with three for 32.
Opener Gary Kirsten, who scored 34, and Neil McKenzie, with 22, shared the biggest stand of the innings -- 39 for the second wicket.
Lance Klusener's unbeaten 34 off 54 balls was the most aggressive batting.
Pace bowling all-rounder Jacques Kallis kept South Africa's hopes alive by dismissing Gilchrist, Mark Waugh and Shane Lee in the space of nine deliveries, reducing Australia to 21 for three in the fourth over.
However, a vigorous fourth-wicket partnership of 83 off 69 balls between Martyn and Michael Bevan took Australia to within 41 runs of victory as early as the 16th over.
Man-of-the-match Martyn blasted 50 off 32 balls with 10 fours before dragging a delivery from paceman Makhaya Ntini onto his stumps.
Bevan was caught by wicketkeeper Mark Boucher off paceman Mornantau Hayward for 39, before Andrew Symonds and Ian Harvey finished the job.