Lasith Malinga returned career-best figures of 5/6 to bundle New Zealand out for 88 while chasing 126.
Lasith Malinga removed Colin Munro, Hamish Rutherford, Colin de Grandhomme and Ross Taylor off consecutive deliveries to reduce New Zealand to 15/4 in 3 overs.
Sri Lanka players Shehan Jayasuriya and Kusal Mendis collided with each other to give New Zealand a six in the final over of the second T20I.
A century partnership between Colin de Grandhomme and Tom Bruce helped New Zealand to a series-clinching four-wicket win over Sri Lanka.
Ross Taylor lifted New Zealand from a precarious 39 for three in their chase of 175 to complete the win in 19.3 overs and lead the three-match series 1-0.
Sri Lanka were bowled out for 122 runs after New Zealand declared their second innings on 431 for six with a first-innings lead of 185.
Contrasting half-centuries from BJ Watling and Colin de Grandhomme helped New Zealand lead by 138 runs in their first innings against Sri Lanka.
New Zealand were 196 for four at stumps, still trailing Sri Lanka by 48 runs.
Sri Lanka posted 144 for six against New Zealand after persistent rain led to early stumps on day two of the second Test.
Only 36.3 overs were possible after rain washed out the first session and bad light ended play for the day with Karunaratne unbeaten on 49.
Shane Warne, who is also a part of the MCC committee which will review the decision, questioned umpire's decision, saying that the overthrow should have been called a dead ball.
Apart from Kane Williamson, New Zealand star pacer Trent Boult will also return home after the two-match Test series against Sri Lanka.
The match officials' report at the end of the first Test between Sri Lanka and New Zealand had expressed concerns about the bowling actions of both players.
Dimuth Karunaratne posted his ninth Test hundred along with enjoying a record-equalling opening partnership of 161 with Lahiru Thirimanne.
Sri Lanka need 135 runs to register a win over New Zealand in the first Test.
At stumps on day three, New Zealand emerged on top thanks to the efforts of BJ Watling, who finished unbeaten on 63.
Tim Southee took 66 matches and 96 innings to achieve the feat while Tendulkar achieved it after playing 200 Tests and batting 329 times.
The ball got trapped inside Trent Boult's helmet in the 82nd over, leaving the players and commentators in all-smiles.