Scrumhalf Antoine Dupont scored a brace of tries as the French side ran in six scores in all, with wings Matthis Lebel and Juan Cruz Mallia, hooker Peato Mauvaka and lock Thibaud Flament also getting over the try-line.
Harlequins were a different team in the second period and pulled to within five points as they scored via flyhalf Marcus Smith, flanker Will Evans, wing Cadan Murley and fullback Tyrone Green.
Toulouse were playing a 16th semi-final and Harlequins their first, and that experience helped see out the contest as a yellow card for visiting hooker Jack Walker gave them the impetus to pull clear in the final stages.
"It was a pretty tense one. Fair play to Quins," Toulouse flanker Jack Willis told ITV. "We know what a quality side they are.
"They threw it at us and it was tough to get the win. You have to stay together and know you have time to get the points back. We have some great leaders, we focused on getting back up the field and on our discipline."
Wings Matthis Lebel and Juan Cruz Mallia, hooker Peato Mauvaka and lock Thibaud Flament also scored tries for the hosts.
The teams traded tries in the early stages, Lebel cantering over in the corner and Mauvaka dotting down for the home team, and Smith and Evans responding for the visitors.
But after that Toulouse began to take control and when Harlequins flanker Chandler Cunningham-South fumbled a loose pass from scrumhalf Danny Care metres from his line, Flament had the easiest of scores.
The hosts' fourth try was via a lightning break after Harlequins had botched an attacking lineout.
Centre Paul Costes beat his defender and put in a perfectly weighted kick that resulted in Dupont diving over, before the latter scored another to give Toulouse a 19-point halftime lead.
Harlequins struck first in the second period when Murley produced a superb finish in the corner, and when Green added another, they closed the gap to five points.
But just when it seemed as though they could create an upset, Walker’s yellow card was followed swiftly by a try for Mallia and the gap on the scoreboard opened up again.
"We messed up in the first half, we gave them too many points and it was too much to pull back," Care said.
"There was a bit of a kick up the bum at halftime. We let ourselves down in a few breakdown areas, we gifted them 28 points, and if you do that it is very hard to pull back."
