At Twickenham Stoop, England full-back Ellie Kildunne scored the first of Quins’ four tries after Scotland international Rhona Lloyd had given the visitors an early lead.
Beth Wilcock, Sarah Parry and Connie Powell secured a try bonus point, although Shona Campbell’s late score set up a nervous finale.
It was announced in May that 22-year-old back row Wafer, the 2025 Women’s Six Nations player of the tournament, would move to Harlequins from Leinster after the Women’s Rugby World Cup.
However, injuries sustained in Ireland’s quarter-final defeat by France in September meant she has had to wait until the seventh round of league fixtures to make her first appearance for her new club.
She came off the bench to play the final 30 minutes.
Quins’ win moved them above Trailfinders, for whom Vicky Laflin scored two first-half tries in their emphatic victory over Leicester.