Opener Jeet Raval was the only batsman capable of any resistance, completing his fourth test 50, and his best test score, 80, as New Zealand lost their last five wickets meekly for just 16 in 36 balls.
Maharaj made good use of the footmarks and his figures meant 12 of New Zealand's 20 wickets in the match fell to spin, when seam bowling had been seen as the major threat.
Between them, Maharaj and offspinner Duminy bowled 50.3 overs in the match; by contrast, New Zealand's sole spinner, Jeetan Patel, took just one wicket in 14.3 overs and didn't appear in the shortened second South African innings at all.
New Zealand scrapped hard to reach 268 in testing batting conditions on the first day.
They then had South Africa 94 for six midway through the second, only for Quinton de Kock (91) and Temba Bavuma (89) to share a 160-run stand, with a further 57 coming from last pair Morkel and Vernon Philander.
New Zealand were simply blown away after lunch today, when three wickets fell in 45 balls before the final late tumble.
Some of the strokes were dreadful and a case could be made that none of New Zealand's six batsmen dismissed by Maharaj had to be really dug out. It was the spinner's second consecutive bag of five or more wickets in the series.
He's now taken 13 wickets at 13.9 each in the three New Zealand innings of this series.
The final test will be at Hamilton's Seddon Park, starting next Saturday.
New Zealand are hoping to have premier fast bowler Trent Boult back, after he missed the second test with an upper leg injury. He had a short bowl in the nets in Wellington today.
Less likely, but a longer shot for Hamilton, is senior batsman Ross Taylor, who damaged a calf muscle in the Dunedin test. He has not yet been officially ruled out of contention.
The defeat is New Zealand's 25th against South Africa in 44 tests, against just four wins, the last of which was at Eden Park in 2004.
