Jesse Ryder limped his way to 59 and Brendon McCullum, fresh from a test best 225 in the second match at Hyderabad, battled a back injury to be unbeaten on 34 as the tourists stumbled to 148 for seven by stumps in their first innings.
Following a delayed start caused by a damp outfield, the day began promisingly for New Zealand as skipper Daniel Vettori won the toss, but it turned ugly from there as opening batsman McCullum almost simultaneously went down with back spasms suffered during warmups.
It prevented McCullum joining Tim McIntosh at the top of the order, with first drop Martin Guptill instead promoted one spot while McCullum remained in the dressing room undergoing treatment.
Team management said only that McCullum would bat lower in the order, and his services were called upon sooner rather than later after New Zealand made a shoddy start to slump to 82 for six barely overs after tea when Gareth Hopkins edged left-arm spinner Pragyan Ojha to slip.
McCullum was clearly in discomfort, running gingerly and regularly stretching his back as he collected a series of singles, while at the other end Ryder went to his sixth test half-century in 131 minutes despite a possible recurrence of a calf strain which flared during his hundred in the first test at Ahmedabad.
He and Ryder put on a stand of 42 for the seventh wicket before Ryder was dismissed after three hours when he slammed a back foot drive off spinner Harbhajan Singh to Suresh Raina at cover.
McCullum resumes today with Tim Southee, who is on seven.
The New Zealanders were lacking the mental sharpness which had served them so well in high scoring draws at Ahmedabad and Hyderabad, McCullum's 11th hour mishap seemingly unsettling their thought processes.
Neither McIntosh nor Guptill stayed around long, both victims of Shantakumaran Sreesanth, who is something of a loose unit but a fast bowler capable of producing quality deliveries.
He came up with two of them to remove the makeshift opening combination in successive overs.
He found a perfect length to induce the thinnest of edges behind from the bat of Guptill on six and McIntosh went next for four when he was beaten for pace by a ball which clipped the top of the off stump.
Ross Taylor, the only specialist batsman not to cash in this series, again missed out after employing his trademark cut to quickly advance to 20.
He was then dragged on to the front foot by recalled fast bowler Ishant Sharma, playing here only because of an injury to left-arm quick Zaheer Khan.
Taylor leaned forward defensively as the ball skidded into his front pad, and Australian umpire Simon Taufel upheld a vociferous appeal despite suggestions that ball struck Taylor outside the line of his off stump.
At 42 for three, Vettori must have had serious misgivings about his decision to bat first.
Those doubts deepened when Kane Williamson came and went in the space of five minutes to make it 43 for four after the 20-year-old scooped up a soft catch to cover off Ojha.
The captain's mood would not have brightened either as he became the next victim for just three.
Vettori had not had time to get his eye in when he attempted to pull a short ball from Ishant outside off only to drag it on to his woodwork.
Earlier, play was delayed for three hours due to a damp outfield at VCA Stadium following a heavy downpour yesterday afternoon.
After taking an early lunch officials announced amended hours of play, with two sessions from 1230 (2000 NZT) to 1440 and from 1500 to 1730.
The wicket block itself was fine but one end of the ground was wet and required a substantial amount of sawdust and light rolling as it remained out of the direct sunlight because of the double decker stand that surrounds the 60,000-seat venue.
Why remedial work was not carried out yesterday following the hour-long downpour is a moot point but workers were outnumbered by supervisors as they went about their duties this morning.
The New Zealanders, too, were in need of supervision.
