Their unimpressive display was livened only by a couple of threatening free-kicks from captain Cristiano Ronaldo.
Coach Paulo Bento said he understood the fans' reaction. "I can't criticise fans who paid their ticket and came to watch a better match and a better result," he told reporters.
"The result was not good and the exhibition was not good but we shoud not be overly concerned."
Portugal, finalists at Euro 2004, will need to be stronger to progress from arguably the toughest group at Euro 2012, where they face Germany, the Netherlands and Denmark.
Macedonia, number 98 in the world ranking and coached by former Liverpool striker John Toshack, were well organised but reliant largely on counter-attacks.
Bento's side play Turkey in a friendly next Saturday, their final test before leaving for Poland.
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