As Malta exhausted, 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.
Harry Kane's second half goal helped Gareth Southgate's men on their way to a crucial win in Group F but it was a frustrating display from the Three Lions.
The Malta team now travels to Scotland for another game to be played on Monday.
But England were flattered by a late flurry of goals in Friday's 4-0 win in Malta, a performance that was accompanied by expletive-sprinkled jeers from their watching supporters. Both of the team having opposite status as England doesn't lose a single match so far.
Danny Welbeck's injury-time goal was lobbed in from a Kane cross, before the Tottenham striker added the fourth to give England a 4-0 scoreline they barely deserved.
"Of course we've got things to improve on".
Southgate added: "Throughout the game Harry was a threat and he will score goals for us".
"You've got to take risks and it's not always going to work but we knew at half-time, keep going, keep persevering and we'll break them down eventually, and thankfully, we managed to score some good goals in the end".
However, England - who next face nearest rivals Slovakia on Tuesday morning AEST - were frustrated by their hosts in the first half at the Ta' Qali National Stadium before Kane finally put them ahead in the 53rd minute.
Credit was due to a manful Maltese effort; they rarely lose by many, but Southgate's team seemed devoid of the ability to break down their opponent. Southgate, whose side remain top of Group F, said: "I've played in nights like this and, if you don't get a couple of early goals, the atmosphere can turn".
"We're by no means the finished article, there's lots of work to do, and we've just got to stay patient as a country together".
Please note that had this match been yesterday Harry would have hit the post, because you know he would have.
"The mood is great, as after every victory, and we will fly in a good mood, but it's important to realise there's a completely different match awaiting us".
"Whenever you come away - games like this - it's never going to be easy from the start", he said.
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