Azam has been unable to overcome an injury to his right hand after being struck by England Under-19 paceman Manny Lumsden during Pakistan's warm-up game last week against a County Select XI. He promptly retired hurt in what a team spokesman said was a "precautionary measure".
It is the same hand he was struck on during the second Test against the West Indies earlier this month.
Azam batted briefly in the Headingley nets on Monday but, while he has been cleared of a broken middle finger, he has not been passed fit to lead the side in the first of a three-Test series.
"Babar Azam is not available, Salman will be captain for the first Test," Pakistan coach Sarfaraz Ahmed told reporters at Headingley on Tuesday.
"It's not broken, there is a little bit of swelling on the finger. Hopefully he will be available for the second Test match."
Azam's absence is a major blow to Pakistan as they begin their quest to win a Test series in England for the first time in 30 years given he is also one of their leading batsmen, with nine Test hundreds and a career average of 43.68.
Saul Shakeel is in line to replace the 31-year-old Azam in the team after missing the recent two-match series in the West Indies, which ended in a 1-1 draw.
Pakistan did win their two most recent Tests against England without Azam on home soil in 2024, but the surface in Leeds is likely to be vastly different to the extremely spin-friendly surfaces in Multan and Rawalpindi.
