Former European champions Hamburg SV were relegated for the first time on Saturday, their fans throwing flares on to the pitch as their team's record uninterrupted top-flight run since the Bundesliga began in 1963 came to a controversial end.
Wolfsburg's 4-1 win over bottom club Cologne meant Hamburg's 2-1 home victory over Borussia Monchengladbach, which was interrupted for 15 minutes due to the crowd trouble in stoppage-time, proved in vain.
"This is an extremely painful moment for the entire Hamburg SV," club president Bernd Hoffmann said. "The club has lost one of its uniquenesses.
"The diamond [club logo] and us as a club are strong despite this current moment and we will in the future again reflect that strength."
Hamburg, six-times German champions and European champions in 1983, will join Cologne in the second division next season, while Wolfsburg go into a relegation play-off.
Dozens of riot police, several on horses, charged on to the pitch and lined up in front of the Hamburg fans, who lit flares and threw them behind the Gladbach goal when it became clear that the team was on their way to the second division.
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Hamburg were leading 2-1 in stoppage-time when referee Felix Brych stopped the game.
The fires were put out and police gradually left the field so the game could resume and the final seconds be played out.
Hamburg had taken an early lead through Aaron Hunt and went in front again with a Lewis Holtby goal just past the hour after Gladbach had levelled before halftime.
Even when Hamburg went down to 10 men after the dismissal of Bobby Wood in the 71st minute, they kept battling, hoping for a miracle but events at Wolfsburg ensured it never came.
With the stadium clock marking the club's record stay in the Bundesliga and showing 54 years and 260 days, fans stayed in their seats and with tears in their eyes gave the players their last Bundesliga cheer.
Borussia 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 - three goals - over Bayer Leverkusen, who conceded two goals against Hanover after leading 3-0, meant they finished fourth and grabbed the lucrative European spot which takes them into the group stage.
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 Stuttgart as they prepare for the German Cup final against Eintracht Frankfurt on Saturday.
Victory for the Bavarians in the showpiece game would mean seventh-placed Stuttgart could compete in the second qualifying round of the Europa League.