But, with just 40 minutes for the Ulster A side prior to that, he has had to miss the following two league games, wins against Leinster and Ospreys.
Ulster face four-time winners Leinster again in the semi-final having lost at the same stage at the RDS in 2011 and 2014 as well as the final at the same venue in 2013.
An Ulster statement read: "Tommy Bowe has had exploratory arthroscopy of his right knee to address discomfort he has been experiencing since the win over Zebre in mid-April.
"The surgery revealed no new injury and Tommy is expected to be fully fit for the start of pre-season."
The two-time Lions tourist picked up the original problem in his right knee during the 2015 Rugby World Cup defeat to Argentina.
He will miss Ireland's tour to South Africa this summer after undergoing his second surgery of the campaign.
Bowe's Ulster team-mate Louis Ludik is also out of the Guinness PRO12 semi-final against Leinster and will undergo surgery on persistent groin pain in England on Thursday.
The utility back described it as "an end to the most frustrating season in my career" on Twitter having not been able to add to his 15 appearances for the season since the first week of February.
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