The International Cricket Council's (ICC) ruling means the 42-year-old is ineligible for the second test in Hamilton, which starts on Friday, though he was already set to miss it having returned home following the death of his father-in-law.
Pakistan were ruled to have been two overs short of their target in the eight-wicket defeat to New Zealand, the ICC said in a statement.
Misbah's ban was mandatory, having previously been found guilty of a minor over-rate offence during the test against England at The Oval in August, the ICC added.
He was fined 40 percent of his match fee and the team 20 percent.
Regular vice-captain Azhar Ali will lead the team in Hamilton, where the touring side will attempt to level the two-match series 1-1.
(Reporting by Ian Ransom in Melbourne; Editing by Peter Rutherford)
