Younis Khan and Misbah-ul Haq also hit dominant tons to put Pakistan in control on 566 for three declared. But Shehzad's injury briefly set alarm bells ringing.Â (Day 2 Report)
In the final over before lunch, Shehzad was hit on the side of the head trying to hook a short ball by New Zealand seamer Corey Anderson on the hard Abu Dhabi wicket.
Shehzad's bat struck the stumps for a hit-wicket dismissal and the dazed batsman fell to the ground before walking off.
Shehzad was later rushed to a hospital where scans showed he had a minor skull fracture and will be kept under observation for the next 48 hours.
Before the drama, he had hit 17 fours and a six in his 371-ball innings.
While team managers worried about the opener, Younis went on to smash an unbeaten 100 -- his 28th Test hundred and fourth in five innings.
Misbah knocked an unbeaten 102, his third ton in three innings. Azhar Ali missed his hundred after he was dismissed for 87.
At the close on the second day New Zealand were 15-0 with Brendon McCullum on nine and Tom Latham on five. They need another 352 to avoid the follow-on.
Younis, who scored 468 runs against Australia in a series which ended last week, hit ten fours in his 141-ball knock.
He hit a century in each innings in the first Test against Australia in Dubai and followed that with 213 in the Abu Dhabi Test last week.
Misbah, who smashed twin hundreds in the second Test against Australia, knocked nine fours and a six off 162 balls.
The two veteran batsmen added 193 for the unbroken fourth wicket stand to build on another second wicket stand of 169 runs between Ali and Shehzad.
Misbah survived two chances, one on 17 and the other on 20 as fielders failed to reach uppish shots with Ish Sodhi the luckless bowler on both occasions.
It was Younis who reached his hundred first, hitting an uppish shot off McCullum which Tim Southee failed to catch at short mid-on.
Misbah drove McCullum in the same over for three to complete his eighth Test hundred.
Pakistan lost Shehzad and Ali in the two sessions after resuming at 269 for one.
Ali missed a sharp turner from Sodhi and was bowled. He hit four boundaries off 215 balls.
Anderson was the best bowler with 2-68 while Sodhi finished with 1-162.
The New Zealanders paid dearly for giving Shehzad a life on Sunday. He had been on 16 when wicketkeeper B.J. Watling failed to stump him off the bowling of spinner Mark Craig.
Craig went wicket-less in his 33 overs.
Shehzad, 126 overnight, took some time to open up on Monday. But he then hit a straight six off Craig before running a three to surpass his previous best of 147 against Sri Lanka in Sharjah earlier this year.
The remaining two Tests will be played in Dubai (November 17-21) and Sharjah (November 26-30).