Kitzingen's record is the highest temperature registered anywhere in Germany since 1881, when comprehensive records began.
News of the new high was confirmed by the German Weather Service (DWD), Bayerische Rundfunk radio reported.
The previous record high of 40.2C was registered in 2003 in Karlsruhe, matching a high from 1983 in Gärmersdorf in the eastern Bavarian Oberpfalz region.
Those records were set in mid-August and late July respectively – raising the prospect that the record might be smashed a second time in a single year.
What to expect this week
While Monday has been cooler after heavy thunderstorms on Sunday night, heat damage to the railways has meant delays for passengers across Germany, especially on the east-west Berlin-Wolfsburg-Hannover line.
And traffic between Essen and Duisburg in North Rhine-Westphalia was interrupted after a lightning strike on railway equipment at Essen's main station.
More storms are expected on Monday evening before a return to extremely high temperatures on Tuesday.
Tuesday's DWD forecast.
Temperatures on Tuesday are expected to reach up to 37C in the south-west, 35C in central Germany and up to 30C in the north, DWD reported on Sunday evening.
A new cold front moving in should reduce highs to between 19C and 25C in the following days before a new uptick at the weekend.