Kansas City made the move less than an hour before Monday's deadline to apply the franchise tag, even though it had long been expected. Bowe is guaranteed a salary of about $9.4 million next season, though the Chiefs have indicated they would like to sign him to a long-term deal.
"Today was the league's deadline to designate a franchise player and we felt it was in the best interest of the Kansas City Chiefs to place the tag on Dwayne," general manager Scott Pioli told the team's official website.
Bowe could still field offers from other teams, but the Chiefs would have the right to match. If they decline, they would lose Bowe but receive two first-round draft picks.
Bowe had 72 catches for 1,162 yards and 15 touchdowns in 2010, when he made the Pro Bowl.
The Associated Press contributed to this report.