In Graz and against one of the two hosts for Euro 2008, Mifsud had plenty of chances. He netted in the 41st when he rounded former Arsenal keeper Alex Manninger.
Malta were 2-1 down at that point with goals for Austria from Aufhauser and Linz.
Three goals from a Linz penalty, Vastic and Harnik in the second half finished off the rout with Mifsud substituted in the 64th minute.
Elsewhere,Scotland lost 3-1 to the Czech Republic.