Sri Lanka post 290-8 against New Zealand in third ODI
The visitors, seeking their first win of the series, had raced to 66 without loss at Eden Park when Nissanka retired hurt with an apparent hip injury.
The right-hander, who was on 50 off 31 balls when he limped off, returned in the 34th over to add a further 16 runs as Sri Lanka posted a competitive 50-over target at the small venue renowned for high scoring.
New Zealand seamer Matt Henry continued a fine series, claiming 4-55 to lift him to 150 ODI wickets, while captain Mitchell Santner took 2-55 with his spin.
The home side are chasing a series clean sweep after winning the second match in Hamilton by 113 runs on Wednesday to follow a nine-wicket victory in the opening game in Wellington.
Sri Lanka's top order struggled badly in both those matches, but Nissanka ensured there would be no repeat as he attacked from the outset in a 42-ball knock that featured six fours and five sixes.
The 26-year-old collapsed to the ground in pain after running a single in the 10th over and his retirement slowed the innings' momentum.
The run rate lifted thanks to 54 off 48 balls from Kusal Mendis before he top-edged Santner while Janith Liyanage held the tail together with 53 off 52.
Sri Lanka named an unchanged side from game two while New Zealand brought in spinner Michael Bracewell for seamer Jacob Duffy.