The Gunners won 2-0 thanks to goals from Ebere Eze and Declan Rice on either side of halftime as they reach the quarterfinals 3-1 on aggregate.
Hjulmand said afterwards: "In the first half, we made too many mistakes in our build-up situations. Arsenal put a lot of pressure on us, but we didn't concede many big chances, just some set pieces, and then Eze scored this fantastic goal.
"I arrived in September and had 14 new players in the squad. We had a bit of a bumpy start and then we did some very good things.
"I think we've played better and better - we went to Benfica and won, we went to (Manchester) City and won, and beat Olympiacos 2-0 in the knockout phase play-offs.
"I think we can be proud of how much we achieved in a build-up season like this. We also see there's a difference between us and the very best in Europe and we are aiming for that, so we can get back into this beautiful tournament and try to compete again. That's our focus."