The game was played to a backdrop of the murderous rampage by the Taliban at a school in Peshawar which left over 140 children and teachers dead on Tuesday.
There was debate whether the match should be postponed in the light of the attack, however the Pakistan Cricket Board said it had to proceed with the game to fulfill obligations with broadcasters and sponsors.
Williamson won his first toss of the series and the batsmen cashed in against a clearly lacklustre Pakistan fielding performance.
Openers Martin Guptill and Dean Brownlie put on a brisk 81, both enjoying some good fortune, interspersed with handsome strokes.
But Williamson was the rock.
He worked the ball impressively around the park, drove sweetly and pierced the onside field neatly.
It was the seventh time in his last nine innings in which he has passed 50, a quality run of ODI form.
His fourth ODI hundred - all of them scored away from home -- anchored New Zealand's innings. Only Nathan Astle (16), Ross Taylor (11), Stephen Fleming (8) and Guptill (5) have scored more ODI centuries for New Zealand.
Williamson's average, 42.34 in 58 matches, is superior to all that quartet.
Taylor was dropped at deep square leg off a rank full toss delivered first ball by part time legspinner Ahmed Shezhad and was not at his best in getting to 26, while Corey Anderson made 23.
One pleasing aspect of the innings was each stand made a decent contribution, producing 81, 44, 63, 39 and 72.
Pakistan's players clearly didn't want to be part of today's game.
There were emotional scenes during the two minutes silence preceding the game, opener Shezhad and Younis the most visibly affected by the events in Peshawar.
Their fielding was lacklustre, there was no celebrating of wickets, most notably absent being captain Shahid Afridi's trademark arms outstretched at the taking of a wicket.
Pakistan struggled early on, losing Shehzad to Henry's second ball, a beauty which struck his off stump.
Speedster Adam Milne had a hugely impressive match, regularly exceeding 150kmph. His first spell of four overs cost just seven and later he removed danger man Shahid Afridi, finishing with one for 39 off his 10 overs.
When Mohammed Hafeez fell to left arm spinner Dan Vettori's first ball Pakistan were 59 for three and well off the pace. Vettori then had Haris Sohail caught at long on and at the halfway mark, Pakistan slipping to 90 for four, and seemingly gone.
However Younis and Umar Akmal had other ideas.
Younis, having got through an awkward examination by Milne, got going, sweeping Vettori for six and lifting Henry over the boundary at long on.
They took 45 in the five powerplay overs but were unlucky when Akmal was run out at the non strikers end, Mitch McClenaghan dropping a sharp return catch by Younis and having the ball glance onto the stumps with Akmal backing up.
That stand of 90 in 89 balls gave Pakistan some hope and Afridi had the ideal platform.
The senior pair got Pakistan onto a par with New Zealand's run rate by the 39th over as Younis completed his seventh ODI hundred, and first in 75 innings.
Afridi clouted Henry for six and Vettori conceded 13 in an over, so with 10 overs left, Pakistan were a chance, needing 89 in the last 10 overs.
Afridi took a glancing blow to the side of his grill, deflecting a Henry delivery off his bat, then slapped a six over long off in the same over as the 50 stand flew by in 31 balls.
Vettori dropped Afridi, a one hand chance over his head at short fine leg off Henry before Milne struck, ending a stand of 66 in 42 balls which showed all the signs of carrying Pakistan to what would have been a remarkable win.
Vettori bowled Younis with his final delivery and with 46 needed off the last five overs Pakistan's chances diminished when the lively wicketkeeper Sarfraz Ahmed skied a catch off McClenaghan.
Vettori finished with three for 53 while Henry, McClenaghan, Milne and Corey Anderson, who left the field after falling awkwardly in the field, took one each.
Williamson was pleased with New Zealand's performance, both with the bat and later in the match with the ball.
''It was just about executing the plans we'd set out for ourselves and formulate those partnerships. It's such a big ground that you can score quite freely, but when you lose wickets it can get quite tough,'' he said.
The teams have one day off before the decider, which also ends New Zealand's tour to the United Arab Emirates.
''It's important we look at it as a one off and try to continue the momentum we've got from this game,'' he said.
Williamson praised Pakistan's persistence today, admitting New Zealand's 299 for five should have been enough for the win.
''Pakistan kept coming and they've shown consistently throughout thi series how good they are. We thought 299 was plenty but they pushed it all the way.''
The decider will be played on the same ground starting late on Friday night (NZT).
