Cowen struck Girgensons in the head late in the third period of Ottawa's game in Buffalo on Tuesday night. No penalty was called on the play.
Girgensons was not injured and later scored the shootout winner for the Sabres. That factored in to NHL vice-president of player safety Brendan Shanahan's decision, as did Cowen's lack of a disciplinary history.
Cowen will miss Thursday's game against Buffalo and Saturday's game against Los Angeles.
The Senators defenceman will forfeit $31,794.88 as a result of the suspension.