With direct rivals Croatia held to a scoreless draw in Azerbaijan, the Azzurri were given extra incentive prior to hosting Bulgaria Sunday in a match that could secure their ticket to next summer's finals in France.
Yet Italy, who had Pelle to thank for their 1-0 win in Malta earlier in the campaign, had to attack a heavily-fortified Maltese backline time and again before Pelle rose to fire in the opener on 69 minutes, although television replays showed the ball could have deflected off his shoulder.
Italy coach Antonio Conte welcomed the win but admitted some of his players were still looking for form.
“We're top of the group. Let's look at who is still fighting fit before we take on Bulgaria,” said Conte.
“We're still at the start of the season and the condition of some players has to improve, but I'm happy with the lads' commitment. They showed their desire to go out and win this match.”
To his credit, Malta coach Pietro Ghedin admitted the validity of the goal was a non-issue: “I didn't see a replay of the goal, but it's not important. The game is finished.”
“Italy are a team that have a lot of charisma. They can score when they want, more or less, but I'm still sorry we didn't get something from this match.”
With Ghedin sticking to his trusted 5-3-2 formation, Conte deployed a 4-3-3 with Manolo Gabbiadini preferred to Candreva on the right of Pelle and Eder on the left of Italy's frontline.
Sampdoria striker Eder, with four goals in two games so far, is Serie A's man of the moment but it was Pelle who earned the lion's share of Italy's chances in a one-sided opening half that saw the hosts frustrated time and again.
In the opening minutes an Andrea Pirlo free kick deflected over and, from the New York City FC midfielder's corner, Pelle just failed to make contact.
A Pelle shot was deflected after a nice touch by Marco Verratti, and the Paris Saint Germain star saw his own drive deflected after good work by Andrea Bertolacci and Eder to keep the ball in play.
From Pirlo's corner, Pelle headed just over in a crowded box.
Malta striker Alfred Effiong came close when he tested Buffon with a curling drive that sneaked past the far post.
But Malta 'keeper Andrew Hogg was by far the busiest 'keeper, parrying a speculative Bertolacci shot with both hands after it took a late deflection.
Italy edged closer to breaking the deadlock when Eder feinted past two players and ignored Pelle's calls on the left to hit a daisycutter that inched wide of Hogg's upright.
Pelle was then unlucky not to make better contact with Leonardo Bonucci's lob, the striker toe-poking wide of Hogg's post, while at the other end Bonucci came to the rescue after Effiong had outpaced Chiellini to threaten down the right.
Conte made no changes at half-time but his instructions to exploit Malta's weakness down the right flank seemed clear.
A spell of Italy pressure saw Pirlo win a free kick 25 metres out, and a well-worked move saw the midfielder slot through to Matteo Darmian, whose shot was blocked.
The ball rebounced to Manuel Pasqual on the left but his shot, too, came off a Malta player.
Marco Parolo replaced Bertolacci soon after and the Lazio forward was unlucky, along with Eder, not to make contact when Darmian whipped an inviting ball in from the right.
Italy were finding more space and Conte's decision to replace Gabbiadini with Candreva unlocked the door.
The Lazio star's pace and ball control had Malta in trouble and minutes after his appearance Candreva delivered for Pelle to beat Hogg at the keeper's near post.