The move, which came less than an hour before the afternoon deadline, guarantees Bowe a salary of about $9.5 million next season. He could still field offers from other teams, but the Chiefs would have the right to match them.
If they refused, they would receive two first-round draft picks as compensation.
Pioli has indicated he would like to sign Bowe to a long-term deal, and the Chiefs have often used the franchise tag as a bridge toward making that happen.
Linebacker Tamba Hali was given the tag last season. Contract negotiations were put on hold because of the lockout, but the two sides eventually agreed to a $60 million, five-year deal early in training camp. The deal made Hali one of the league's highest-paid pass rushers.
The decision to use the franchise tag on Bowe had been expected ever since the Chiefs agreed to terms with cornerback Stanford Routt on a $19.6 million, three-year deal last month.