Black Caps wicketkeeper-batsman B-J Watling said the most similar incident he had experienced was stopping for the 2012 Olympic sprint finals during drinks when playing in Jamaica.
"I can't say I've ever had that happen before, though. The bigger shame was that the crowd left. It was a cool atmosphere out there."
Play resumed after a 20-minute delay.
The Fire Service indicated the alarm in the stand might have been set off by steam, but that was yet to be proven.
Play resumed after a delay of approximately 20 minutes.
South Africa were 14 for one when the match was halted. They finished on 38 for one at stumps, a lead of five runs.
New Zealand made 341 in their first innings in response to the Proteas' 308.
Dunedin Venues spokesperson Kim Barnes said the cause of the fire alarm was unknown at this time.
"In accordance with health and safety procedure and the emergency management plan, the venue was fully evacuated until the all clear was received by the NZ Fire Service."
