Bowe scored two tries in the 47-17 win over Zebre on 16 April, his first appearance of the season for Ulster after being ruled out by the injury since the Rugby World Cup in October.
Number eight Nick Williams has played his last game for the province.
Williams will undergo surgery on his shoulder injury this week.
The Kiwi back-rower has been unsuccessful in his bid to rehabilitate his recent shoulder injury and will undergo surgery to repair a labral tear.
The former Pro12 player of the season will miss the remainder of the season and will turn out for Cardiff Blues in the next campaign.
These two latest injury setbacks will come as a major blow to Ulster coach Les Kiss, who is already faced with a lengthy list of absentees.
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Prop Wiehahn Herbst has begun to reintegrate into team training sessions and the province's medical staff are confident he will be available for selection within the next two weeks.
Full-back Louis Ludik remains unavailable for selection as he continues his recovery from a groin injury, while Ian Humphreys has seen a spinal specialist and had a recent injection for his ongoing back injury.
Second row Alan O'Connor had surgery 10 days ago following his recent shoulder dislocation, but is expected to be fit for the beginning of next season.
Centre Sammy Arnold is continuing rehabilitation from a hamstring injury but is unlikely to be available for the remainder of the campaign.
Dan Tuohy (ankle), Peter Nelson and Willie Faloon (both midfoot) continue to rehab their respective season-ending injuries.
Ulster lie fourth in the Pro12 table ahead of their final two fixtures against Leinster and the Ospreys.
Ulster winger Tommy Bowe will miss Saturday's key Pro12 game with Leinster at Kingspan Stadium after suffering a reaction to his knee injury.