New Zealand are up against it with three days remaining in their second test against South Africa at Centurion.

The hosts declared at 481 for eight, then had New Zealand reeling at 38 for three at stumps on day two.

New Zealand's bowlers deserved more but it was an innings where edges were beaten, not found, and they were unable to make sufficient inroads, having sent South Africa in to bat.

Captain Faf du Plessis made an unbeaten 112, but had slices of luck along the way.

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New Zealand lost openers Martin Guptill, fending to slip, and Tom Latham, caught behind, before Ross Taylor ran himself out for just one, setting off for a quick single, then turning back to be beaten by Temba Bavuma's direct hit from mid wicket.

''We're not in an ideal position," senior seamer Tim Southee said in a heavy dose of understatement.

''It was pretty tough for the bowlers. But we've been in a similar position before."

''As a group we felt we passed the bat a fair bit. It was just one of those days where the ball almost did a little too much at times and didn't catch the edge."

The only New Zealand bowler to prosper was bustling left armer Neil Wagner, who took five for 86 off 39 overs playing in the city of his birth, and his former home ground.

He earned high praise from Southee, who with Doug Bracewell and spinner Mitchell Santner finished with one wicket apiece.

''Neil has been outstanding for a long period of time. He's reaping the reward for the effort and the tough overs he's bowled for the majority of his career.

''Nine times out of 10 he'll get the ball when it's a bit older and the wicket a bit flatter and he'll run in and make something happen from nothing. Today was no different.

''He keeps giving for the team and that sums him up as a person. He never gives up."

So far on New Zealand's African test tour, Wagner has taken 19 wickets at an outstanding 16.8 each, easily the best return of any New Zealand bowler over the course of the tests in Zimbabwe and South Africa.