The number hit 100 after rising from 68.7 just eight days ago, the Robert Koch health institute (RKI) said.
The milestone comes a day after the German health ministry warned that "we are seeing an escalation of the situation".
The upwards trend "became visible in almost all age groups over the past week and it is to be expected that the increase in case numbers will pick up speed in the further course of autumn and winter," health ministry spokesman Oliver Ewald said.
Germany recorded 86 new Covid-19 deaths on Saturday, with the country's total toll rising to 95,077, official figures said.
There were also 15,145 new infections recorded over 24 hours, the figure having risen 31 percent over the last eight days.
The health ministry said Friday that the spike in cases had not yet led to an "increased dynamic" in Covid patients needing intensive care.
Germany's DIVI intensive care association however voiced alarm.
Senior DIVI expert Christian Karagiannidis wrote on Twitter that there was a "very close correlation" between incidence rates and new Covid hospital admissions.
"The real fourth wave is beginning now and is gathering speed," he tweeted.
More than 66 percent of the population of Germany, a country of some 83 million people, is fully vaccinated against Covid.
Almost 70 percent have had a first dose.