Frankfurt won 3-1 at rivals Freiburg and Dortmund eased past already-relegated Holstein Kiel 3-0 thanks to Serhou Guirassy, Marcel Sabitzer and Felix Nmecha, leaving Freiburg in a Europa League spot having yet again narrowly missed out on the Champions League.
Dortmund have rocketed up the table in recent weeks under Niko Kovac, having been 11th when he was appointed in January.
"If you had said in March that we would be in the Champions League, people would have said you were stupid. We are very, very happy," Dortmund captain Emre Can told Sky.
"Mentality has been key. Niko is someone who cares about the small details," Can added. "He is a bit old school. He has really helped."
Mainz edged RB Leipzig to the Conference League slot after a 2-2 draw at home to Bayer Leverkusen sealed by Jonathan Burkardt's penalty.
Leipzig will not be in Europe for the first time since their Bundesliga debut in 2016-17 following a shock 3-2 home defeat by mid-table VfB Stuttgart, who can grab a Europa League spot by beating third-tier Arminia Bielefeld in next Saturday's German Cup final.
Heidenheim needed a large goal difference swing to pull St Pauli or Hoffenheim into trouble and avoid finishing third-bottom in the play-off spot. The 4-1 home defeat by mid-table Werder Bremen made any mathematics irrelevant.
St Pauli lost 2-0 at home to already-relegated Bochum and hosts Hoffenheim were beaten 4-0 by long-crowned champions Bayern Munich, whose departing veteran Thomas Muller played what is set to be his last Bundesliga game while Harry Kane got on the scoresheet one last time this campaign.
The 35-year-old Muller recently wrapped up a record-extending 13th Bundesliga title but will not stay in the German top flight out of respect for his so far only club Bayern.
"People have been bidding me farewell for six weeks," he joked to Sky about the time since his exit announcement.
"It was a lot of fun. The time was crazy. The Bundesliga has always been my league, to play so many games is obviously nice.
"I wanted to score but only to win the game, not as a farewell goal. Football is about winning."
Muller made his Bundesliga debut for Bayern way back in 2008 and has made 503 league appearances. He might still turn out for Bayern at the Club World Cup from mid-June but is then widely expected to go to the MLS, also in the United States.
Meanwhile, Kane finished the season as Bundesliga top scorer for the second straight campaign with 26 goals, saying afterwards that winning the title this time made the honour much sweeter.
"It is what I have been waiting for. It is a special feeling," he said after netting off the bench. "It was nice to finish with another goal."
Heidenheim will face the third-placed team in the second tier - currently Elversberg - over two legs on Thursday and the following Monday for a place in next season's Bundesliga.
SV Hamburg have already secured promotion and Cologne are favourites to join them on the second-tier's final day on Sunday.
In two games with nothing to play for, Borussia Monchengladbach were undone 1-0 at home by Wolfsburg while Union Berlin overcame Augsburg 2-1 away in storied referee Felix Brych's last game.
