The latest measures will come into effect from November 2 until the end of the month after Germany announced a record high Wednesday of 14,964 new cases in the last 24 hours.
Since the 2020/21 Bundesliga season started in mid-September, Germany's football clubs had been allowed to host small numbers of fans for home games, providing each local health authority granted permission.
One noticeable exception is European champions Bayern Munich, who have had to play all their home games at the Allianz Arena behind closed doors since the pandemic first hit Europe in mid-March on advice of the local health authority.
But from Monday all professional sport in Germany will go back behind closed doors after Merkel and the regional leaders of Germany's 16 states agreed to the new measures.
Borussia Dortmund's Champions League home match against Zenit Saint Petersburg on Wednesday must also take place without fans on site.
The health authority in North Rhine-Westphalia rejected an application to allow 300 fans into the 81,000-capacity stadium for the European game.
"That makes me sad," admitted Dortmund CEO Hans-Joachim Watzke after around 300 Dortmund fans were allowed to watch last Saturday's 3-0 home league win over Schalke.