Gareth Southgate's side struggled to break down physical, resilient opponents and it was 53 minutes before Harry Kane broke the deadlock with a calm close-range finish from Dele Alli's pass.
As Malta tired, England exerted their authority and Ryan Bertrand sealed the win with a long-range shot that slipped past Malta goalkeeper Andrew Hogg with five minutes left.
England - who are now two points ahead of Slovakia as they prepare to meet at Wembley on Monday - began to carve Malta open with ease and added two more in injury time, substitute Danny Welbeck steering in Kane's pass before the striker added his second with virtually the final kick of the game from Marcus Rashford's delivery.
