The Germans, drawn in the World Cup alongside Australia, Ghana and Serbia in the group stage, were missing 12 key players, including Bayern Munich and Werder Bremen players as well as captain Michael Ballack on duty with Chelsea.
Germany found little resistance from lowly Malta but missed scores of chances with keeper Justin Haber in good form.
"The result is too few goals," said Germany coach Joachim Low. "We played well, carved out chances and that was positive but we squandered too many of them."
"Some players were missing, we knew that. I wish I had them all at the start of our World Cup preparation for four weeks straight. Now we must do it in two weeks and work as a team," Low told reporters.
Cacau, who netted 13 times for VfB Stuttgart in the league this season, broke the deadlock in the 16th minute when Dennis Aogo crossed from the left and the striker headed in for the lead.
Cacau only became eligible to play for Germany last year after taking up German citizenship.
The striker, who is assured a place in the World Cup squad as all six of the nominated strikers will be included, grabbed Germany's second in the 58th when Lukas Podolski combined well with Kevin Grosskreutz to cut into the box for the unmarked Cacau.
Veteran Kenneth Scicluna scored an own goal two minutes later when he misjudged a Podolski pass to fire into his own goal from two metres, before Stefan Kiessling missed a few more chances for Germany to increase the scoreline.
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