The Italian outfit clinched a 2-0 victory on Finnish soil against Allianssi and matched the scoreline they achieved at Renato Curi last week.
A first half effort from Fabio Gatti set Perugia on their way and Ze Maria's goal on 69 minutes settled the match.
Perugia's semi-final opponents will be Nantes, who earned a 5-3 aggregate success over FC Wil after a 3-2 win in Switzerland.
The French side were trailing 2-1 after goals for the hosts from Umberto Romano and Felix Mordeku sandwiched a Mario Yepes strike.
But Marama Vahirua put Nantes back in the driving seat just before the interval and a second half goal from Gregory Pujol eased the nerves.
Racing Santander were dumped out of the competition by Slovan Liberec after suffering their second defeat to the Czech Republic side.
Slovan won the first leg in Spain 1-0 and were in control of the second leg on 35 minutes when Vaclav Kolousek scored.
Txiki put Racing back in the tie on 54 minutes but a late goal from Tomas Zapotocny extinguished any hopes of a comeback.
In one of the tastier ties in the round, Villarreal moved into the semi-finals after grinding out a 1-1 draw at Brescia to seal a 3-1 aggregate win.
Werder sneaked into the semi-finals at the expense of French outfit Nice after a 1-0 triumph at home.
Johan Micoud's 27th minute strike proved to be the only goal of the whole tie and put Werder one step nearer to qualifying for the Uefa Cup.
Schalke also advanced into the semi-finals after a 2-1 success over Dacia Chisinau with goals from Ebbe Sand and Mike Hanke making sure of their progress.
Wolfsburg joined their German rivals in the semi-finals after easily disposing of the threat of FC Synot.
Diego Klimowicz and Martin Petrov bagged the goals to give Wolfsburg victory and a semi-final showdown with NK Cibalia.
The Croatian outfit could afford a 1-0 home defeat to Tampere United as they held on for a 2-1 aggregate triumph over their Finnish foes.
Guingamp failed to progress after taking a 2-1 advantage to Czech Republic for their second meeting with FC Brno.
A late goal from Brno's Svoboda sent the match into extra-time with the hosts eventually claiming a 4-2 triumph in the contest.
Heerenveen were never in danger of losing sight of their European dream after taking a 4-1 advantage into the second leg of their tussle with Benelux rivals Lierse.
A last minute goal from Romano Denneboom secured another win for Heerenveen and a semi-final meeting with FC Koper of Slovenia.
FC Koper squeezed into the semi-finals after the Slovenian side overcame Greek club Egaleo 5-4 on aggregate.
Pasching will play Werder Bremen in the next round after a 3-0 home win over Tobol Kostanay sealed a 4-0 aggregate triumph.
InterToto Cup Third Round Results (aggregate scores in brackets):
Pasching 3-0 Tobol Kostanay (4-0)
Allianssi 0-2 Perugia (0-4)
FC Koper 2-2 Egaleo (5-4)
FC Wil 2-3 Nantes (3-5)
Werder Bremen 1-0 Nice (1-0)
Brescia 1-1 Villarreal (1-3)
FC Brno 4-2 (AET) Guingamp (5-4)
Schalke 2-1 Dacia Chisinau (3-1)
Slovan Liberec 2-1 Racing Santander (3-1)
Wolfsburg 2-0 FC Synot (3-0)
NK Cibalia 0-1 Tampere United (2-1)
Lierse 0-1 Heerenveen (1-5)
