Left-arm pacer Trent Boult helped New Zealand counter Pakistan's advantage with four wickets as the first Test was evenly poised after day two in Abu Dhabi.
Boult's four wickets derailed the Pakistani batsmen who were bowled out for 227 in response New Zealand's first innings total of 153.
Debutant spinner Ajaz Patel picked up two wickets as Pakistan got a first innings lead of just 74.
New Zealand then finished the day at 56-1 when bad light forced umpires to end the day.
The Kiwis now trail by 18 runs with still nine wickets intact.
The duo of Williamson and Raval added 56 for the second wicket after Tom Latham was bowled by Hasan Ali on first ball of the second over.
Pakistan lost a good chance of taking a big lead through some poor shot selection, with Babar Azam (62), Asad Shafiq (43) and Haris Sohail (38) making contributions.
Azam struck five boundaries in his 109-ball 62 and was the last man to be dismissed when he got a faint tickle down the leg side.
Pakistan started the second day at 59-2 but lost overnight batsmen Haris Sohail and Azhar Ali in a space of just six balls.
Azhar was dropped by Jeet Raval off Boult on 19 and was again lucky two runs later when given not out as the fast bowler reviewed for a leg-before decision.
Boult again lured Ali into a wide ball which was caught by Watling - diving low to his right.
Pakistan were well-placed at 144-4 at lunch, seeking a big lead to get a 1-0 advantage in the three-match series.
But Boult checked Pakistan’s progress by dismissing Asad Shafiq for 43 as he was found guilty of being tentative in his decision-making. That dismissal started a batting collapse that saw Pakistan's last six wickets fall for just 63 runs.
Shortly, Patel had Sarfraz Ahmed caught off a miscued sweep for two and Bilal Asif stumped by Watling for 11.
Wagner later on removed Yasir Shah to claim his 150th Test wicket.
The second Test will be played in Dubai (November 24-28) and the third in Abu Dhabi (December 3-7).