Costa, who played 66 minutes of Spain's 1-0 friendly defeat against France in Paris on Thursday, had tests in Madrid that revealed an injury in his left thigh, Spain said on their official website.
The test results would be sent to Costa's club Chelsea and Spain medical staff had already been in touch with their counterparts at the Premier League side, they added.
The inclusion of Under-21 international Munir, who turned 19 on Monday, is something of a surprise as he only made his debut for Barcelona in their opening La Liga match at home to Elche last month, scoring in a 3-0 win.
Born near Madrid, he is of Moroccan origin and joined Barca's youth academy in 2011.
Spain host Macedonia in Valencia on Monday and their qualification Group C also includes Ukraine, Belarus, Slovakia and Luxembourg.
(Reporting by Iain Rogers, editing by Rex Gowar)
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