Pakistan, who began the tournament by beating Sri Lanka at the weekend, lurched to 4-81 and 5-133 but were bailed out by Arafat's 59 and Hasan Nawaz, who belted four sixes and five fours in his 79.
Both were dropped. Gus Atkinson spilled Nawaz on 30 in the deep and Jordan Cox, deputising behind the stumps for Jos Buttler, missed a harder chance to dismiss Arafat on 12.
Pakistan added 91 in the last 10 overs enabling them to rack up 9-302.
"At the halfway stage, we were pretty happy," England's white-ball captain Harry Brook said. "I thought we kept them to just below par and we executed our plans exceptionally well and unfortunately we didn't manage to get it quite right with the bat.
"The story of the innings was not enough partnerships and losing wickets in clumps. We didn't manage to put their bowlers under enough pressure to make them miss and that's something we'll talk about.
Tom Banton and Ben Duckett shifted the momentum in England's favour with a 91-run opening stand.
But Arafat turned the tide again by dismissing the in-form Banton and the 21-year-old, in his fifth ODI, breached the defences of Brook, before the slow left-armer took out England's lower order.
Arafat claimed a career-best 6-40 and effected the run out which sealed Pakistan's win as England collapsed from 5-197 to 214 all out in 38.4 overs – long before the dew became any kind of factor, which had prompted Brook to field upon winning the toss.
England's openers had initially been measured against Pakistan's vaunted quicks although Banton (57) twice pulled Naseem Shah for six before Duckett (45) was bounced out by Haris Rauf.
Minhas then dismissed Banton and followed against Brook (5) with one that gripped in the surface, turned and clipped the top of off-stump. A beauty to prise out a player who averages 70 in Pakistan.
Root (33) and Sam Curran (27) rebuilt against Pakistan's spinners but were dismissed when the quicks came back.
Cox (18) and Will Jacks (19) next added 20 but after the former was lbw off Arafat England capitulated ending with a messy run out with both Atkinson and Sonny Baker at the non-striker's end.
"It feels like that's the most convincing loss we've had since last year sometime. It's a good sign in one way but we've got tonight and tomorrow to talk about it and get ready for Sri Lanka on Thursday," added Brook.
England follow the tri-series with a white-ball tour of Australia as teams build towards the 50-over World Cup in southern Africa in 12 months' time.
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