Considering Malta had taken just one point from nine previous matches in the qualifying campaign, it was the expected outcome, and now Portugal must look to maintain their momentum going into next month's double-header against another group runner-up.
The Portuguese have recovered well after a dismal first half of their bid to reach South Africa, and will surely now fancy their chances of reaching the finals, given they will be among the seeded teams in next Monday's draw.
Goals from Nani, Simao Sabrosa, Miguel Veloso and Edinho made it a comfortable evening for Carlos Queiroz's side in Guimaraes.
The result means that Sweden will not be going to South Africa, despite a 4-1 win over Albania.
That results brought to an end the reign of coach Lars Lagerback who had previously announced his intention to stand down should Sweden fail to qualify.
He at least signed off with a solid win as Olof Mellberg netted twice and Marcus Berg and Anders Svensson also got on the scoresheet. Hamdi Salihi got the goal for Albania.
Denmark, with qualification already secured, laboured in a 1-0 defeat to Hungary at home, Akos Buzsaky getting the decisive goal after 35 minutes.