Naib, 21, hit a 93-ball 100. He added 93 with Mirwais Ashraf who made 37 as the pair guided Afghanistan to 207-9 in their 50 overs.
Pakistan ‘A’ knocked off the required runs in 41.3 overs.
The two teams play a Twenty20 here today.
Mumbai Roundup: 9 incidents that took place this week
Photos: Ajay Devgn, Parineeti, Tabu at 'Golmaal Again' trailer launch
Photos: Dipika Pallikal Karthik oozes oomph in bikinis and sarees
Photos: Kareena Kapoor Khan's grand birthday bash
Photos: 'Dangal' girls Sanya Malhotra, Fatima Sana Shaikh's dinner outing