It was announced earlier on Tuesday that Luis Enrique would not be at the game due to a family emergency, though there never looked to be any danger of an upset under the guidance of assistant Robert Moreno.
Although it took them longer to make the breakthrough than they would have wished, Morata put Spain ahead in the 31st minute, with Malta having just 16 per cent of the ball in the first half.
The visitors continued to underwhelm despite their dominance in the second half, though Morata doubled his tally towards the end to wrap up a comfortable – albeit unimpressive – victory.
Spain unsurprisingly dominated proceedings and Saul Niguez looked their most likely route to goal. The midfielder shot agonisingly wide from distance in the 16th minute, shortly before slicing a more presentable opportunity over from 12 yards out.
Morata made no such error just past the half-hour mark, however, racing on to Mario Hermoso's pass and beating Henry Bonello – who got a hand to the ball – from a tight angle.
Spain stepped things up again around the hour, going close three times in as many minutes, Morata sending a header just wide before Marco Asensio forced Bonello into two smart saves.
But Bonello was helpless 17 minutes from time, as Morata rose to meet the cross of Jesus Navas – introduced for Saul a few moments earlier – and finish Malta off.
What does it mean? Debate about lack of goals unlikely to go away
In Luis Enrique's pre-match news conference, he dismissed the idea Spain are not scoring enough goals, pointing out they averaged 2.7 goals per game in his seven matches at the helm, a better record than Barcelona in LaLiga this term.
However, a 6-0 win over Croatia skews that statistic, and an inability to really put minnows Malta to the sword suggests there might be an issue the Spain boss needs to address.
Morata makes his mark
Few of the Spain players really impressed in Malta, but Morata was the one to make the difference, doing particularly well with the goals and generally leading the line well. There was little he could do about the often-poor service, though that did not stop him getting a double.
Bernat offers little
Deployed on the left flank ahead of Jose Gaya, Bernat looked a little awkward after spending most of his senior career as a full-back. He was unsurprisingly withdrawn for Iker Muniain early in the second half.
When Euro 2020 qualifying resumes in June, Spain will face Faroe Islands away from home, while Malta go to Sweden.