Southee injured his left foot in his first over of the ODI against the Sri Lankans at Nelson last Thursday. Scans have shown bruising on a bone in the foot.
''Tim was feeling really fresh after coming back from a break for the first two ODIs, so it's certainly disappointing for him that this has happened now," New Zealand coach Mike Hesson said today.
''He's obviously a key member of our team and has been a strong performer in all three formats, so he's a big loss.''
No firm date has been set for his return, but his progress will be monitored. In-form seamer Matt Henry takes his place in the squad to face Sri Lanka in Mt Maunganui tomorrow, and at Eden Park on Sunday.
New Zealand have three further T20s against Pakistan when their visit starts next week.
