The tourists racked up 289-7 in their 50 overs at Malahide with Neil Broom hitting 79 and Ross Taylor adding 52.
A third-wicket stand of 86 between O'Brien (109) and Andrew Balbirnie (36) gave Ireland hope but they collapsed from 212-5 to 238 all out.
New Zealand spinner Mitchell Santner (5-50) took five wickets.
Ireland's opener against Banglasdesh on Friday was washed out.
The Black Caps were captained for the first time by Tom Latham, while Central Districts fast bowler Seth Rance and Northern Districts all-rounder Scott Kuggeleijn made their debuts.
Luke Ronchi (37) and Latham (15) put on 53 for the opening partnership and it was a solid platform from which New Zealand capitalised.
Taylor and Worker (50) put on an unbroken 84 before Broom's impressive knock helped to set a target of 290 for the hosts.
Barry McCarthy (2-59) and Tim Murtagh (2-62) were the pick of the Irish bowlers.
O'Brien failed to get the support required to take Ireland close to the target but it was a superb innings, which included nine boundaries and five sixes in 162 balls.
Ireland were 26-2 after debutant Kuggeleijn (3-41) accounted for openers Williams Porterfield (12) and Paul Stirling (14).
Gary Wilson contributed 30 but when Santner had O'Brien stumped by Ronchi, leaving the Irish on 235-8, it signalled the end of the run chase.
"It was a nice nice milestone personally but without the win it's gutting," said wicketkeeper O'Brien.
"We were in a great position in our innings and it was just a just a case a case of moments not going our way.
"I'm delighted to get that performance - it was a long time coming and hopefully I can crack on from here."
It was a game against his home country for Ireland coach John Bracewell, who featured in 41 Tests and 53 one-day internationals for New Zealand before coaching the national side between 2003 and 2008.
The series sees the Irish continuing their countdown towards possibly being handed Test status next month.
Niall O'Brien's maiden ODI century was not enough to prevent Ireland falling to a 51-run defeat by New Zealand in the Tri-Nation Series.