Argentine forward Julian Alvarez scored a 90th-minute goal to win the game for Atletico Madrid.
The gap at the top of the Bundesliga table is down to four points between Bayern Munich and Bayer Leverkusen.
In 2024, football's uncertainty reached a height it hasn't scaled in many years.
Bayern Munich were dumped out of the German Cup by holders Bayer Leverkusen as Nathan Tella's second-half goal secured a 1-0 win for the Bundesliga champions on Tuesday.
Boniface is Leverkusen's highest scorer in the league, with six goals and an assist in 10 games.
Leipzig's 2-1 loss at Dortmund last week, their first in the league this season, has given Vincent Kompany's Bayern the chance to grow their lead at the top of the table.
Liverpool's return of 12 points means they are almost certainly already assured of a place in the knockout phase, but are closing in on sealing direct progression to the last 16 via a top-eight finish in the 36-team league.
Bayer Leverkusen coach Xabi Alonso said it was "too early" to write off his side's title defence despite dropping more points in Saturday's 2-2 draw at Werder Bremen.
Xabi Alonso's side now have 11 points from six matches, giving Bayern Munich the chance to extend their advantage at the top.
Bayern remain top of the Bundesliga table, two points ahead of RB Leipzig and three ahead of Leverkusen.