England won the toss and batted first, reaching 172-8 from their 20 overs, with James Vince top scoring with a sprightly 38 from 24 balls, while Jos Buttler (33) and opener Jason Roy (29) also contributed.
The Pakistan chase appeared to be faltering until Afridi arrived at the crease with the hosts on 120-6 with a little over three overs remaining and smashed 24 runs off eight balls that included three sixes and a four.
Having dragged Pakistan back to within 25 runs of victory with two overs remaining, Afridi's march was halted and England were able to breathe a sigh of relief as he sliced a Chris Woakes delivery to Liam Plunkett.
Woakes then removed Sarfraz Ahmed with Pakistan needing 11 from the final five deliveries, but when Sohail Tanvir smacked a four off his first ball, a thrilling finale appeared to be in store.
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England, however, managed to turn off the taps and restricted Tanvir and Anwar Ali to just three runs from the final four balls, leaving them short of their target on 169-8.
The victory was England's fifth consecutive Twenty20 success heading into the World T20 in India in March.
"It's a bit more stressful being captain but it was a performance full of character. We didn't play our best, Afridi played as only he can but we got over the line," stand-in captain Buttler said.
The final match in the series takes place in Sharjah on Monday.
(Reporting by Toby Davis; editing by Ken Ferris)
