The new law was made possible by a surprise vote in the Parliament three months earlier.
"We're making a single exception to fire a symbolic starter pistol because same-sex marriages are possible from today," The Independent quoted Gordon Holland, a registrar in Berlin's Schoeneberg district, as saying.
About 60 guests and an equal number of journalists packed into Schoeneberg town hall's "Golden Room" to witness the marriage of Karl Kreile and his partner of 38 years, Bodo Mende.
Kreile, 59, told The Independent it was an "incredible honour" to be the first same-sex couple to marry in Germany, noting that he and Mende, 60, had been campaigning for gay rights for decades.
Their wedding cake featured a rainbow flag and the words "marriage for all". The couple have now planned to hold a small reception and fly to Vienna later in the week for a five-day honeymoon.
Germany introduced registered partnerships in 2002, but those gave same-sex couples fewer rights than heterosexual couples who married.
Chancellor Angela Merkel had long opposed same-sex marriages, only agreeing to a free vote in Parliament on the matter in June, shortly before national elections.
The bill, which enjoyed strong public support, passed by a wide margin, with 393 lawmakers voting in favour of marriage equality and 226 - including Merkel - voting against. (ANI)