Pakistan decided to rest Taufeeq, top scorer in the recent Test series win over South Africa in which he made 111, 61, 68 and 71, due to a chronic knee injury.
But Imran Farhat, who shared three successive century opening stands with Taufeeq against South Africa, is retained in the one-day squad, which includes experienced opener Saleem Elahi, recalled after being dropped from this year's World Cup.
The New Zealand team arrive on November 28 in Lahore under a revised itinerary.
The Pakistan board has retained Inzamam-ul-Haq as captain
"Shoaib obviously would be playing in the last three matches and he is a regular member of the team so he will remain with them," chief selector Aamer Sohail told Reuters.
The Pakistan squad also includes rookie fast bowler Junaid Zia, who has been recalled after a disappointing showing in four matches against Bangladesh.
The Pakistan squad: Inzamam-ul-Haq (Capt), Imran Farhat, Saleem Ellahi, Yasir Hameed, Yousuf Youhana, Shoaib Malik, Abdul Razzaq, Azhar Mahmood, Moin Khan, Danish Kaneria, Shabbir Ahmed, Muhammad Sami, Shoaib Akhtar, Misbah-ul-Haq and Junaid Zia.
