Nissanka had been scoring at a blistering pace, reaching his half-century in just 31 balls. However, his celebration was short-lived as he suddenly collapsed on the ground, clutching his groin or hip in agony.
He tried to bat on but was clearly impaired while running between wickets and was 50 not out when he was summoned from the field by Sri Lanka coach Sanith Jayasuriya to receive medical treatment.
Nissanka returned when Sri Lanka was 183-4 in the 34th over, after Kamindu Mendis was out for 46. He hit two fours and a six, adding 16 runs to his total before he was out in the 37th over when Sri Lanka was 204-5.
Sri Lanka's top order finally fired Sunday after having failed to do so in the first two matches of the series which New Zealand won by nine wickets and 113 runs to take an unassailable 2-0 lead in the series.
On Saturday, after Sri Lanka won the toss, Nissanka and Avishka Fernando had put on 66 for the first wicket before Nissanka was forced to retire hurt.
Fernando struggled to 17 from 33 balls and was out soon after Nissanka's retirement.
But Kusal Mendis and Kamindu Mendis kept up the momentum of the innings, adding 87 for the second wicket. Kusal made 54 from 48 balls with two fours and thee sixes and Kamindu 46 from 71 deliveries.
The New Zealand pacers tried to use the bounce of the Eden Park drop-in pitch but that opened up the square boundaries for the Sri Lanka batters who hit 15 sixes.
After Nissanka's dimissal Janith Liyanaga made a half century from 51 balls with three fours and two sixes and was out for 53 as Sri Lanka added 76 runs from the last 10 overs.
Matt Henry took 4-55 for New Zealand.
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