Right-arm pacer Tongue is the only inclusion in the hosts’ XI.
Ali had been struggling with a finger problem during his return to testing at Birmingham last week.
The 25-year-old Tongue made his Lord’s debut earlier this month against Ireland.
He also sacked Steve Smith at county cricket earlier this year.
The decision means England have chosen not to spin the legs of teenager Rehan Ahmed.
Joe Root, the world’s highest ranked Test batsman, will also have to provide England’s main spin option.