Malan is the club’s sole representative in a squad that includes nine uncapped players after England’s plans for the three-match series which starts on Thursday were thrown into chaos after three players and four staff members tested positive for Covid-19, forcing the rest into self-isolation.
There were four Yorkshire players in the initial party - Joe Root, Jonny Bairstow, Adil Rashid and David Willey.
Ben Stokes will captain the side having been absent from international duty since breaking his finger at the Indian Premier League earlier this year.
The uncapped players are Brydon Carse, Zak Crawley, Lewis Gregory, Will Jacks, Tom Helm, Dan Lawrence, David Payne, Phil Salt and John Simpson, although Crawley, Gregory and Lawrence have played for England in other formats.
There is no recall for Nottinghamshire batsman Alex Hales, who has not been involved since being axed from the World Cup squad in 2019.
ECB chief executive Tom Harrison said: “We have been mindful that the emergence of the Delta variant, along with our move away from the stringent enforcement of bio secure environments, could increase the chances of an outbreak.
“We made a strategic choice to try to adapt protocols, in order to support the overall wellbeing of our players and management staff who have spent much of the last 14 months living in very restricted conditions.
“Overnight we have worked swiftly to identify a new squad, and we are grateful to Ben Stokes who will return to England duties to captain.”
The 10-day isolation period spans all three ODIs at Cardiff on Thursday, at Lord’s on Saturday and at Edgbaston next Tuesday. England then play three Twenty20s against Pakistan at Trent Bridge on July 16, at Headingley on July 18 and at Old Trafford on July 20.
New squad: Ben Stokes (Durham, captain), Jake Ball (Nottinghamshire), Danny Briggs (Warwickshire), Brydon Carse (Durham), Zak Crawley (Kent), Ben Duckett (Nottinghamshire), Lewis Gregory (Somerset), Tom Helm (Middlesex), Will Jacks (Surrey), Dan Lawrence (Essex), Saqib Mahmood (Lancashire), Dawid Malan (Yorkshire), Craig Overton (Somerset), Matt Parkinson (Lancashire), David Payne (Gloucestershire), Phil Salt (Sussex), John Simpson (Middlesex), James Vince (Hampshire).