The match began an hour late as the fallout rumbled on from a handshake row with India.
The Pakistan Cricket Board was considering pulling out from the tournament after their demand to remove Andy Pycroft who oversaw Sunday's game, after which the India team refused to shake hands with their rivals.
The International Cricket Council refused the change and Pycroft officiated the UAE match.
Fakhar Zaman scored 50 off 36 balls and Shaheen Shah Afridi added a brisk 29 not out as Pakistan made a modest 146-9 batting first.
Spinner Abrar Ahmed led Pakistan's bowling charge with 2-13 as the UAE were dismissed for 105 in 17.4 overs. Shaheen took 2-16 and fellow paceman Haris Rauf 2-19.
The win means Pakistan join India in the Super Four from Group A. They will meet again in Dubai on Sunday.
Rahul Chopra top-scored for the hosts with a run-a-ball 35.
Pakistan got off to a shaky start as Saim Ayub fell for a second-ball duck while Sahibzada Farhan made five, both falling to pace bowler Junaid Siddique.
Siddique finished with an impressive 4-18 in his four overs.
Zaman and Salman Agha added 61 for the third wicket. Agha made 20.
Zaman hit three sixes and two fours before he fell to left-arm spinner Simranjeet Singh, who took 3-26.
It was left to Shaheen to help Pakistan add 51 in the last five overs.
Sri Lanka meet Afghanistan in Abdu Dhabi to decide who goes through to the next round from Group B. Bangladesh are also in the running with two wins in three matches.
