Bayern Munich were toppled from the league summit after drawing 1-1 with Schalke 04.
Schweinsteiger's challenge on Schalke's Larsen led to the penalty
Danish international Soren Larsen won the questionable spot-kick and then converted it to peg back Bayern and the dropped points allow Werder Bremen to replace Bayern at the summit on goal difference.
"Who is first, second or third is not that important at the moment," said Bayern handler Felix Magath. "When it gets to around Christmas that is the time to start looking at the top of the table."
With 93 minutes gone it looked like Bayern would retain their position at the Bundesliga summit after Paraguayan international Roque Santa Cruz had put the visitors ahead after 19 minutes.
Bayern had never won at the Arena Auf Schalke since the venue opened in 2001 - losing their last five matches in Gelsenkirchen - but were preparing to celebrate before referee Weiner awarded the suspicious penalty.
Bastian Schweinsteiger was adjudged to have fouled Larsen and the Dane got off the floor to thrash the ball in and leave Munich coach Magath raging on the touchline. "It was never a penalty," said Magath. "But we only have ourselves to blame as we should have made it 2-0 to relieve the pressure."
Weiner sent off Bayern's Argentine midfielder Martin Demichelis in the fourth minute of injury time for a mistimed tackle as the visitors' afternoon went from bad to worse.
Ten-man Munich almost claim victory
Santa Cruz gave Bayern the lead early on
Schalke played with more urgency in the opening exchanges but Bayern deservedly took the lead on 19 minutes. Brazilian Ze Roberto cut a cross back from the left and Paraguayan striker Santa Cruz slotted home for his second Bundesliga goal in succession.
Schalke came out stronger in the second half with Brazilian playmaker Lincoln watching compatriot Lucio deflect his shot over the crossbar.
But it looked like Schalke had run out of ideas until Larsen won the penalty in the dying seconds and his goal ensures Schalke remain the only unbeaten team in the German top-flight.
"We wanted to beat Bayern but will settle for the 1-1," explained Schalke coach Ralf Rangnick.
Werder go on rampage to claim top slot
Klose's was one of the weekend's many hat-tricks
Bremen hammered FC Nuremberg 6-2 at the Weserstadion with German international Miroslav Klose scoring a first half hat-trick to take his season's tally to ten.
"We took all our chances today and scored some great goals," said Bremen manager Thomas Schaaf. "I am happy with the points and the results of our rivals are a bonus too."
It was indeed a day for hat-tricks with two players scoring all the goals in the thrilling 3-3 draw between Kaiserslautern and Borussia Dortmund.
Dortmund let lead slip to draw in six-goal thriller
Smolarek did half the scoring in the 3-3 draw
Polish international Ebi Smolarek must have thought he had won the game for Dortmund scoring three times inside the first 40 minutes, but Turkish star Hamit Altintop responded with a treble of his own.
SV Hamburg could have gone top themselves but fell to a surprise 1-0 home defeat against VfL Wolfsburg and slip to third, two points behind Bayern and Bremen.
Netherlands international Rafael van der Vaart, one of the stars of the season so far, was sent off for Hamburg after the final whistle for pushing an opponent as players from both sides clashed near the centre circle. "The international break appears to have disrupted our rhythm," explained Hamburg boss Thomas Doll. "We looked jaded and unfortunately we failed to take any of our goal scoring chances."
Skibbe tastes defeat from Bayer's poisoned chalice
Neither Skibbe nor Völler have enjoyed success lately at Leverkusen
Elsewhere Michael Skibbe did not enjoy his managerial debut at Bayer Leverkusen with his side tasting a 3-1 defeat at Mainz 05. Skibbe, Germany's assistant coach to Rudi Völler for the Euro 2004 finals, is the third man to sit in the Leverkusen dug-out this season after Klaus Augenthaler's dismissal and Völler's brief spell as interim boss.