McClenaghan tweeted after the match "Thanks for all the concerns. Everything is as good as it can be just a few broken bones".
Nicholls, in his sixth ODI, gave the hosts' innings spine, making 82 off 111 before chopping on to Ali. The remainder of the top seven scored 47 with no-one getting more than 11. Nicholls' man-of-the-match innings propelled New Zealand back into the contest to post 280 for eight.
He was dropped on 15 by Mohammad Hafeez at first slip, flailing at a short-of-a-length Ali ball. The gaffe proved costly.
The hosts' total also received a boon when Matt Henry swung four sixes in a 48-run, 30-ball cameo. They reached a run rate of five for the first time in the 47th over. Henry and McClenaghan put on 73 runs for the ninth wicket, a record against Pakistan. Two extraordinary scoops from McClenaghan (31 from 18 balls) added garnish before his injury.
The New Zealand bowlers were accurate from the outset. Fresh from a duck, Grant Elliott produced nagging line and length and cunning slower balls to secure three for 43 from his 10 overs.
In McClenaghan's absence he, Corey Anderson and Mitchell Santner each contributed their fair share of overs. Trent Boult also excelled as the newly-anointed world No.1 ODI bowler, taking four for 40 from nine overs. The catching was sound with eight pouches on the scorecard.
Pakistan's formidable pace attack of Mohammad Irfan, Mohammad Amir, Ali and Wahab Riaz swarmed over the New Zealanders early. The hosts risked delivering their worst ODI batting performance in more than two years.
Their lowest completed total in the Mike Hesson coaching era is 156 against the West Indies at Eden Park on Boxing Day, 2013.
However, the 79-run, seventh-wicket partnership between Nicholls and Mitchell Santner (48 off 63) extracted them from the mire. The benefit the pair will derive for their futures in the New Zealand team is impossible to underestimate. They knuckled down when it counted.
The highlights were in Pakistan's column for the first half of the innings.
Irfan (2-43) generated formidable bounce, Amir (3-28 from 8.1 overs) tempted with swing before leaving the field after taking a ball in the left shin, Ali (3-66 from 9.5 overs) drew multiple false shots and Riaz brought bustling aggression despite remaining wicketless.
A capacity crowd bore witness to a team mesmerised by outstanding bowling partnerships in the first 26 overs.
Irfan and Amir had New Zealand 41 for two after nine overs, Ali and Riaz took two wickets for 35 from the next nine before the quartet combined for two for 38 from the following eight.