Italy dominated from the outset at the Ta'Qal stadium but ultimately failed to turn chances into goals as Malta, who saw Michael Mifsud sent off before the half hour, kept bodies in defence for long periods and sought to break on the counter-attack.
Pelle's performances in the English Premier League this season had caught the eye of Italy coach Antonio Conte, who lined the big striker up alongside Ciro Immobile in the hope his powerful physique would provide extra options up front.
Pelle was a constant threat in the Maltese box and saw a first-half header smack off the crossbar from one of several inviting crosses by Fiorentina midfielder Manuel Pasquale.
But despite his winner and the precious three points that mean only Italy and leaders Croatia are unbeaten in Group G, Pelle indicated there was little cause for celebration in the Azzurri camp.
"I'm happy I scored and we got the three points but we have to do better," he told Sky Sport Italia.
"I'm used to playing in England where you play to score goals."
Although Conte was happy with a third win after defeating Norway (2-0) and Azerbaijan (2-1), he expects Italy to raise their game for Croatia in Milan next month.
"The big game against Croatia will tell us just how good we are after these first two months," Conte said.
"We need to get down to work if we're to succeed."
As early as the first minute, Immobile flashed a shot just wide of Andrew Hogg's upright after latching onto Antonio Candreva's cross.
Italy were frustrated for the opening quarter hour but the hosts managed to give Gianluigi Buffon a scare when Giorgio Chiellini, who scored all three goals including an own goal in a 2-1 win over Azerbaijan on Friday, gave away a free kick on the right.
The ball was whipped into the area and as Mifsud fell under a challenge from Leonardo Bonucci it rolled out to Clayton Failla, whose deflected
daisycutter went just wide of Buffon's far post.
Italy were soon back in command, however, and Pelle's powerful header from Pasquale's delivery came back off the crossbar, with Chiellini's header from the resulting corner also hitting the woodwork.