Dortmund, who endured a rollercoaster season and as recently as February were in last place, staged a superb comeback in the past months to rescue some pride from an otherwise disappointing campaign.
They were in equally fine form against rivals Werder for much of the game as the 80,667 fans gave Klopp a standing ovation both before and after the game.
A huge banner reading "Thank You Juergen" unfurled by the "Yellow Wall", the standing section housing 25,000 fans, before the start set the stage for a celebration of the club's last-gasp achievement and the coach's successful spell.
Shinji Kagawa and Pierre-Emerick Aubameyang scored within two minutes before Levin Oztunali cut the deficit for the visitors.
Henrikh Mkhitaryan restored their two-goal cushion and a late goal from Theodor Gebre Selassie did not rattle Dortmund who hung on for victory.
"It is sort of fitting for our season to turn this game into a nail-biter towards the end," Klopp told reporters. "But I think overall it was a fully deserved victory. Now I want one day to come here to this stadium and watch a game in peace."
"I always wanted to leave behind a solid basis when I decided to go. It was an honour for me," he said after an emotional lap of honour in front of adoring fans.
The 47-year-old German coach, who is set to take over a top European club next season with half a dozen wanting to sign him, had announced his departure earlier this season after conceding the team needed changes to return to the top of the league.
Klopp, who took over in 2008, has long been a crowd favourite with the team's success on the pitch coinciding with their financial revival after being on the brink of bankruptcy in 2005.
He led them to the 2011 Bundesliga and the 2012 domestic league and Cup double as well as reaching the 2013 Champions League final where they lost to Bayern Munich in the first and only all-German final of the competition.
He can now add one more title to the club's trophy cabinet, with Dortmund facing Wolfsburg in the German Cup final in Berlin.
Win or lose the Ruhr valley club, however, is guaranteed a place in Europe with their opponents having already qualified for the Champions League after finishing second in the Bundesliga.
(Reporting by Karolos Grohmann; Editing by Douglas Beattie)
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