Bowe, 32, played in the first half of the game in Naas and came through unscathed before being replaced at half-time as had been the plan.
The Lions star had been out since sustaining a knee injury in Ireland's World Cup defeat by Argentina.
Bowe suffered posterior cruciate ligament and meniscal damage.
His return is a timely boost as the Belfast club attempt to secure a place in the Pro12 play-offs.
Les Kiss's men are currently fifth in the standings and have three matches left, against Zebre, Leinster and Ospreys.
Darren Cave captained the Ulster A team as they earned a 38-31 win in Thursday's game.
Ireland winger Tommy Bowe played his first match since October in the Ulster's A game against their Munster counterparts on Thursday.