Southee leads New Zealand charge to have Pakistan on the ropes
Azhar Ali will resume on 34 with Fawad Alam on 21.
The Black Caps need to sweep the two-Test series if they are to be in contention to make the World Test Championship final at Lords in June.
Although Pakistan are out of the running for the final they are keen to improve their world ranking of seven. But their cause was not helped when the wizardry of Southee and swing partner Trent Boult removed both openers for nought.
Azhar Ali and Haris Sohail provided some resistance for 15 overs and 37 runs before Southee was back in action.
He broke the partnership with a full delivery to Sohail (9) which was chipped to Mitchell Santner at short cover -- making Southee only the third New Zealander, after Richard Hadlee and Daniel Vettori, to take 300 Test wickets.
Southee has two for 15, and Boult one for 24. Neil Wagner, who was thought to have broken one toe while batting on Sunday, but has now been diagnosed with a second broken toe, sent down six overs to have none for four.
- Wickets fall -
New Zealand began their second innings at the start of the day with Tom Latham and Tom Blundell putting on 98 in the first session.
Mohammad Abbas briefly troubled Latham, who sent three edges towards the slips, while a loud lbw appeal against Blundell was turned down with the TV umpire unable to distinguish whether the ball hit bat or pad first.
Otherwise the batsmen were untroubled, with Yasir Shah getting six overs but unable to produce any turn of note.
After lunch it was clear the declaration was approaching as New Zealand dropped their risk-free approach and wickets fell as the total rose.
Blundell was bowled for 64 when trying to slog Abbas over midwicket and New Zealand were 111 for 1.
Eleven overs later they were five for 170 as Pakistan bought wickets with a short-ball approach.
Latham, who had feasted on ones and twos and ran on misfields to keep the scoreboard ticking over, opened up with a textbook cover drive to the boundary to reach his 20th half-century.
He was dismissed soon after for 53 when he mistimed a pull shot and was caught in the deep.
Kane Williamson's attempted pull shot was top edged to wicketkeeper Mohammad Rizwan and he was gone for 21, while Henry Nicholls went for 11 when his pull shot was caught by Abbas at fine leg.
For Pakistan, Naseem Shah was the most effective bowler with three for 55.
New Zealand 1st innings 431(K. Williamson 129, B. Watling 73, R. Taylor 70, H. Nicholls 56; Afridi 4-109, Yasir Shah 3-113)
Pakistan 1st innings 239 (F. Ashraf 91, M. Rizwan 71; Jamieson 3-35, Wagner 2-50)
New Zealand 2nd innings
T. Latham c Abid Ali b Naseem Shah 53
T. Blundell b Abbas 64
K. Williamson c Rizwan b Naseem Shah 21
R. Taylor not out 12
H. Nicholls c Abbas b Naseem Shah 11
B. Watling run out (sub/Rizwan) 5
M. Santner not out 6
Extras (lb2, w1, nb5) 8
Total (five wickets dec; 45.3 overs)180
Fall of wickets: 1-111 (Blundell), 2-139 (Latham), 3-147 (Williamson), 4-165 (Nicholls), 5-170 (Watling)
Bowling:Afridi 11-0-47-0 (1w), Abbas 11-2-33-1 (1nb), Naseem Shah 12.3-1-55-3 (4nb), Ashraf 4-1-18-0, Yasir Shah 6-0-21-0, Masood 1-0-4-0
Pakistan 2nd innings
S. Masood c Taylor b Southee 0
Abid Ali c Watling b Boult 0
Azhar Ali not out 34
H. Sohail c Santner b Southee 9
F. Alam not out 21
Extras (b4, lb2, w1) 7
Total (three wickets; 38 overs) 71
Fall of wickets: 1-0 (Abid Ali), 2-0 (Masood), 3-37 (Sohail)
Bowling: Southee 9-5-15-2, Boult 10-4-24-1 (1w), Jamieson 7-6-3-0, Wagner 6-3-4-0, Santner 6-1-19-0
Umpires: Chris Gaffaney (NZL), Wayne Knights (NZL)
TV Umpire: Chris Brown (NZL)
Match Referee: Jeff Crowe (NZL)