Former Liverpool midfielder Keita was told before Sunday's trip to Leverkusen he would not be in the starting XI. He refused to board the team bus and instead went home.
"We won't tolerate Naby's behaviour," Bremen sporting director Clemens Fritz said in a statement, saying the club had "no alternative."
"He let his team down in a time of difficulty surrounding our recent run of form and squad availability and put his own interests above those of the team. We can't allow that."
Keita, joined Liverpool from RB Leipzig for a fee of 60 million euros (£51m) and won the Champions League and Premier League with the Reds, but was often injured.
He moved to Bremen as a free agent in the summer of 2023 but has played just five matches in all competitions and is yet to score or lay on an assist. Earlier this season, Keita played four matches in Guinea's run to the quarter-finals of the Africa Cup of Nations.
Bremen sit 12th but are just five points clear of 16th-placed Mainz, who are in the relegation play-off spot.
