Matsui, 33, prepared to head back to New York during the Yankees' 11-10 victory over the Orioles at Camden Yards and will miss the club's regular-season finale on Sunday.
Yankees manager Joe Torre said that the procedure is not expected to change Matsui's status for the American League Division Series, which will begin for the Yankees next Thursday at Cleveland.
"It's nothing that is serious, but there was enough fluid in there to want to drain it," Yankees manager Joe Torre said.
Torre had said recently that he intends to use Matsui as a designated hitter throughout the playoffs, citing Johnny Damon's fresher legs in left field.
The knee issue had been a long-standing concern for Matsui, who batted just .185 in 81 September at-bats. The Japanese icon completed his fifth Major League season batting .285 with 25 home runs and 102 RBIs in 142 games for New York.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.