Bowe was one of the stars of the 2009 Lions tour of South Africa and touched down four times in six appearances.
But he has been hit with a knee problem which could result in an extended period on the sidelines.
"We've withdrawn Tommy from this weekend's game on medical grounds, pending further investigation and specialist opinion for a knee problem," said Ospreys head physio Chris Towers.
"Due to the onset of some recent symptoms we scanned him this week, which highlighted an issue that could potentially develop into something problematic.
"As such, we felt that it is in Tommy's best interest to take these precautions.
"We have notified the Irish medical team, and following further investigations next week we should be able to establish the most appropriate course of treatment for the problem, and to confirm whether it will interfere with Tommy's involvement in the Six Nations with Ireland."