The Croatian forward scored twice on his Gunners comeback against Cardiff City in the FA Cup on Monday night, five days after setting up the winning goal for his country in a 2-1 win against Romania.
However, the Brazilian-born front-man, who had been out for almost a year, is now expected to be missing for around two weeks after suffering a minor hamstring injury.
"Eduardo is out for two weeks," manager Arsene Wenger told the club's official website.
"He picked up a hamstring injury two minutes before I took him off. What a nightmare. Nobody knows how it happened but I knew straight away after the game it would be a two-week job.
"It is nothing like he had before but I do know that little setbacks like this are part of being nine months out. After that long out, nobody plays six months on the trot. It is impossible.
"But at the same time it is a blow because, of course, he can score goals. He had shown that on Monday night."
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