The Bosman-ruling signing from Manchester City was sent off while playing for their reserves at the end of last season.
Football league rules state that if a player cannot complete a suspension because the league campaign ends, it must follow on.
Whelan, who was one of Chris Turner's first signings this summer, has impressed while playing for the Republic of Ireland Under-21 team and it is expected that the all-round midfielder will be a key player in the 2004-05 season.
Wednesday could appeal against the ban although it is unlikely that anything will come of it.
Meanwhile, released Mark Robins may be tempted to come out of retirement to play for Burton Albion.
The non-league team, for who Des Walker played after he left Wednesday, are coached by Nigel Clough and depending on how Robins' knee holds out, he may give the veteran striker a deal next season.