A first-half double from Mario Balotelli ensured Italy secured all three points but they were thankful to Buffon, who marked his 126th Azzurri cap in style. The Juventus shot-stopper kept a clean sheet and prevented the hosts from equalising in the 16th minute when he saved expertly from Michael Mifsud's spotkick.
Speaking to reporters after the match, Prandelli said: "Buffon marked this landmark like a captain with a great save at the crucial moment."
After an impressive fightback against Brazil last Thursday, Prandelli had hoped for another convincing display but witnessed a rather lacklustre performance from his side.
"We take away an excellent performance against Brazil and these three points. When there are no spaces and a team is very organised, we must learn to be quicker in our build-up.
“We knew there would not be spaces and were perhaps a little too slow in construction, so ran into trouble. We still maintained possession throughout the game. We lacked a bit of intensity in the finishing.
“We were too distant between defenders and midfielders, so the passes got misplaced. It may seem absurd, but the wind affected the long passes too.
“We did some things well, others not so well. We must learn from this that against clammed-up teams we have to pass the ball short and quick.”
Riccardo Montolivo was also keen to pay tribute to the performance of his Milan team-mate Balotelli who has now scored 10 goals in nine games for club and country in 2013.
"Malta were clammed up and it was tough to find spaces. Luckily we had that superstar in attack and he sorted it out for us.
“I think Mario has become fully aware of his abilities and has learned not to fall into the trap of provocation. He has had a remarkable impact on Milan too and I hope he won’t stop.
“Balotelli is a centre-forward and is therefore the leading point of the attack. We can even give him the ball badly, as he is so physically strong that he can hold off defenders and find space. Right now, he is a complete player."
Montolivo concluded by praising Serie A clubs Milan and Juventus, who between them, made up the complete starting 11 for the Azzurri - the first time the national side has comprised of players from solely two clubs since 1947.
“It means these two teams focus on home-grown talent, so that is a good sign for Serie A and the Nazionale."
Bulgaria's 1-1 draw with Denmark ensured that Italy moved three points clear at the top of group B. Cesare Prandelli's side return to qualifying action away against Czech Republic on June 7.