Gloucester will get home advantage in the tie having achieved a superior points total. The Cherry & Whites managed 16 points from their four games, their only blemish coming against the Dragons in the first game of the pool stages.
But they bounced back with wins against Saracens and Leeds Carnegie before sealing their safe passage through to the knockout stages with a seven- try demolition of London Irish.
Harlequins, though, progress as first seeds after a 23-7 win over Cardiff Blues lifted them to the top of Pool D on 17 points. It was their ninth straight win in all competitions and a first over the Blues in five attempts.
Nick Evans contributed 18 points with a try, two conversions and three penalties as Harlequins finished the group stages as the only side with a 100% record from their four qualifying games.
Newcastle Falcons now stand in their way after topping Pool A courtesy of a last- gasp win over Exeter Chiefs. Tries from Alex Tait and Luke Eves settled the contest in the last few minutes.
The semi-finals are as follows:
Harlequins v Newcastle Falcons - Friday March 11, 2000
Gloucester Rugby v Newport-Gwent Dragons - Sunday March 13, 1300
The final will take place on Sunday March 20, KO 1530. Venue tbc.