England went ahead after only eight minutes at Wembley Stadium
Phil Foden's pull-back was diverted into his own net by Malta defender Enrico Pepe after only eight minutes, but Gareth Southgate's side failed to register a single shot on target in the opening hour against a nation ranked 171st in the world.
However, England did produce a bit of quality in the 75th minute to seal victory through Harry Kane.
It came after a fine one and two-touch passing move involving Kyle Walker, Foden and Bukayo Saka, who set up skipper Kane for his 62nd international goal.
Declan Rice thought he had added a third, excellently curling low into the bottom corner, but the goal was ruled out following a check by the Video Assistant Referee (VAR) as Kane, standing in the goalkeeper's line of sight, was adjudged offside.
Chelsea forward Cole Palmer made his debut in the second half at a packed national stadium.
England had qualified for next summer's Euro 2024 in Germany with two games to spare, but only five of the 10 group winners, along with the hosts, will be seeded when the draw is made next month.
Southgate's side play their final qualifier on Monday in North Macedonia and a draw would be enough to guarantee a top seeding.
-- Courtesy of BBC Sport