On Thursday evening, Frederik Birk's troops won 1-0 over HB Torshavn from the Faroe Islands after a 1-1 draw in the first match a week ago. This means that Brondby advances 2-1 on aggregate.
Brøndby's new Japanese player, Sho Fukuda, scored the winning goal that gave them the slender advantage.
Sho Fukuda was in the starting lineup for the first time for the Danes, and he showed several examples of his explosive pace.
After exactly half an hour, Marko Divkovic broke into the box and delivered a fine delivery to the front post, where Fukuda was left with an easy tap-in to open the score for the Danes.
Divkovic and Clement Bischoff were responsible for most of Brondby's build-up through the left side, where the vast majority of Brondby's crosses arrived from.
Brondby played at high speed in the first half, which was the key against the compact and defensively-minded away team.
That created enough opportunities to put the home side solidly in control before the break, but they lacked the decisive final touch, and the woodwork saved both attempts from Daniel Wass and Clement Bischoff.
Brondby struggled to regain their stylish stride in the second half, with chances appearing more sporadically.
The club's other new Japanese player, Kotaro Uchino, who was substituted for compatriot Fukuda midway through the second half, should have doubled the lead, but missed the open net with the goal at his mercy.
Instead, the home side got nervous, and with a little luck, Torshavn could have forced the game into extra time.
Brondby will be in action in the third round of the qualifiers next Thursday, where they will face the winner of the meeting between Albanian side KF Vllaznia and Vikingur Reykjavik from Iceland.