The Argentine boss was able to take heart from a home defeat to the Bundesliga side, although admitted his disappointment at exiting the competition
Having been beaten 3-0 in the first leg, Pochettino's side were hoping for a miracle in front of their own fans at White Hart Lane on Thursday in the last 16 of the competition.
Yet a fine long-range strike from Pierre-Emerick Aubameyang midway through the first half put the tie beyond Tottenham, before he added a second goal for the visitors in the 71st minute.
The hosts did get a consolation from Son Heung-min, who made the most of Neven Subotic's weak back pass to round goalkeeper Roman Weidenfeller and score, but they can now focus on their bid to win the Premier League.
"I'm very disappointed we're out of the Europa League, but we need to recognise we played against a very good team [playing at] a Champions League level, because Borussia Dortmund are one of the best teams in Europe," Pochettino told BT Sport.
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"I think we improved a lot, learned a lot from last week in Germany. We competed and we need to take positives.
"We have a lot of young players that need to feel what it means to compete in Europe and I think for the team it was a good test and we can take positive things."
Midfielder Ryan Mason admitted Tottenham had simply left themselves with too much to do after conceding three goals without reply in Germany.
He also praised a Dortmund side who are yet to lose in 2016 and have now won all four of their knockout ties in the Europa League this season.
"The first leg killed us," Mason told BT Sport.
"The tie was over to be fair. We didn't do ourselves any justice. We didn't go there and get our philosophy across.
"We were punished big time by a top side. There's no doubt about that – they're a top side."