Second match takes place at the same venue on Monday, before the finale in Auckland, as both teams step up their preparations for the men's T20 World Cup.
Green Shirts were once again guilty of conceding early goals, and despite having levelled the match, they were eventually undone by Markham's strike three minutes from time.
Pakistan and New Zealand share a point each as South Africa becomes the second team to qualify for the semis; Green Shirts still search for their first win.
Gandapur did not cross certain red lines and that might have been his undoing, while Afridi said his top priority was to secure the release of Imran and his wife.
