Former European champions Hamburg were relegated from the Bundesliga for the first time despite a 2-1 win over Borussia Moenchengladbach.
Borussia Dortmund scraped into fourth place and a Champions League spot in the season finale while Bayern Munich were thrashed as they lifted the league trophy for the sixth-straight time.
Hamburg, the only team with an uninterrupted Bundesliga run since the league's creation in 1963, left their distraught fans in tears as their stadium clock showing 54 years and 260 days in the top division needs to be reset.
"We experienced miracles in the last years but miracles don't go on forever," Hamburg great Uwe Seeler said.
The northern club, whose game was interrupted for 15 minutes by fans throwing flares on to the pitch near the end, finished second-bottom on 31 points, two behind Wolfsburg, who beat Cologne 4-1 and face second-tier Holstein Kiel in a relegation/promotion two-legged playoff.
Dortmund were made to sweat until the last seconds to secure the final Champions League spot after losing 3-1 at Hoffenheim, who grabbed third place ahead of them on goal difference.
Dortmund's marginally better goal difference over Bayer Leverkusen, who beat Hannover 3-2, meant they finished fourth and grabbed the lucrative European spot which takes them into the group stage.
But it was the last Dortmund match for coach Peter Stoeger, who confirmed his widely-expected departure less than six months after taking over.
"We had decided some time ago that the club would benefit from fresh stimulus," Stoeger told reporters.
"That can happen easier with a new coach. Today was my last game for Dortmund."
RB Leipzig's Jean-Kevin Augustin scored twice in their 6-2 demolition of hosts Hertha Berlin as they joined Leverkusen in the Europa League.
Champions Bayern Munich suffered a surprise 4-1 home loss to VfB Stuttgart as they prepare for the German Cup final against Eintracht Frankfurt on Saturday.
But there was still plenty of celebrating in Munich as they lifted the Bundesliga trophy and forward Robert Lewandowski was crowned top scorer for the third time with 29 league goals.
"There are days like these," Bayern coach Jupp Heynckes said after his last home game before retirement.
"Now we have to dust ourselves off, deal with the loss and prepare from Tuesday for the Cup final. You will see a different Bayern team in Berlin."
Victory for the Bavarians in the Cup final would mean seventh-placed Stuttgart could compete in the second qualifying round of the Europa League.
Elsewhere, second-placed Schalke edged Eintracht Frankfurt 1-0, Freiburg accounted for Augsburg 2-0 to seal their top-flight status and Mainz lost 2-1 to visiting Werder Bremen.