Charles Boateng scored first in the 24th minute when he connected home from close range but Medeama equalized seven minutes from the halftime whistle through a Justice Blay header inside the box.
In the 57th minute, Kwesi Donsu smashed in a superb volley from the right flank to seal the points for the Tarkwa-based.
''We lost to every good team. They played us very well. We didn't have the weapons to stop them, I would say they made two very good goals,'' Rasmussen said in the post-match interview.
'The opportunities we had, were not big enough so I congratulate the [Medeama] players for a very good game.
''Last year we played 0-0 and we were in trouble so I think on this pitch they are very good.''
It was the first home defeat for WAFA since 21 January, 2015 when they were beaten 1-0 by AshantiGold.
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