The result at White Hart Lane sealed a 5-1 loss on aggregate for Spurs, who fail to reach the quarter-finals of Europe's second-tier tournament for the third consecutive year.
The tie was all-but over as a contest following last week's 3-0 defeat in Germany but Tottenham restored some pride during a closer second leg.
Pierre-Emerick Aubameyang extinguished any slim hopes of a comeback for the home side with a stunning early strike and the Gabon forward scored another in the second half before Son Heung-min added a consolation.
Spurs may have to face teams of similar quality to Dortmund more regularly next year if they qualify for the Champions League and Pochettino believes his players are ready to step up.
"I am disappointed because we are out of the Europa League but we need to take the positives," Pochettino said.
"We learn a lot from this tie. We play against a team at Champions League level and for that we take positives.
"In the first leg we didn't play well, we didn't compete how we normally compete, but today from the beginning of the game we showed we can compete at this level."
Pochettino rested key players again, starting Harry Kane on the bench and leaving Christian Eriksen, Mousa Dembele and Kyle Walker out of the squad completely, with Bournemouth to come in the league on Sunday.
Eric Dier did start, and looked to be struggling with an injury late on, while Ben Davies was forced off early in the match after a nasty collision with Hugo Lloris.
Davies was allowed to continue for five minutes by Tottenham's medical staff before the full-back finally decided to come off.
"Ben is okay now," Pochettino said
"We need to assess him for concussion in the next few days
"He got a knock in his face and after the knock he came into the pitch again, started to feel dizzy and we took him off as a precaution."
On Dier, Pochettino added: "He has a knock but we hope he will be okay for the weekend."
Dortmund have their own title challenge to consider as they sit second in the Bundesliga, also five points off the top.
Thomas Tuchel, however, picked another strong side despite his team's commanding lead at kick-off and he believes too much focus on Pochettino's team selection is unfair.
"It's unfair to make that comparison and perhaps insults our achievements over the two games," Tuchel said.
"I'm sure my colleague thought his team was capable of winning. We deserved to win both games. I don't think you can talk about line-ups as a, b, or c."
Dortmund go through to the quarter-finals where they could now face Jurgen Klopp's Liverpool and few would bet against the German outfit going on to lift the trophy in Basel in May
Tuchel, however, was keen to dwell on this win over Tottenham for as long as possible as he asked for extra time at his post-match press conference to add one last anecdote
"As a little kid in my garden when I played I was always a team from Bundesliga of course but the one team I was when I played with my friends was Tottenham Hotspur because I liked the name so much," Tuchel said
"I had not a picture, I didn't even know they played in London. So for me to play them in two legs was very special
"And what I didn't know as a kid, what I felt today and yesterday, is there are so many friendly people here and around the club
"The coaching staff from the team and all the staff around the stadium were unbelievable , such great support, and such a great atmosphere - it made us feel very welcome so thanks a lot and all the best for the club."
Source: PA