"Michael Keane has been handed his first international call-up after Glen Johnson withdrew from the England squad through injury," the FA said in a statement on its website.
Manchester City winger Raheem Sterling was earlier forced to withdraw with an injury and was replaced by Crystal Palace's Andros Townsend.
Keane last week said a national call-up would be the pinnacle of his career.
"Now I'm in the Premier League I think England has got to be my aim. I want to play at the top level of English football and playing for England is the pinnacle of that," the 23-year-old told Burnley's matchday magazine.
England host Malta at Wembley Stadium on Saturday before travelling to take on Slovenia three days later.
England pipped Slovakia 1-0 in their opening Group F game last month. The group also includes Scotland and Lithuania.
(Reporting by Ian Rodricks in Bengaluru; editing by Amlan Chakraborty)
