The female Shin Shin and her companion Ri Ri were put in a private enclosure on Monday evening after keepers at Ueno Zoo in Tokyo noticed they were ready to mate.
"We have confirmed Shin Shin and Ri Ri mated on Monday evening and Tuesday morning," Hidetoshi Kurotori, an official at the zoo's education and information division, said. "Things are moving ahead smoothly."
Kazuomi Nishikiori, director of education and information at Ueno Zoo, declared himself delighted with the animals' progress.
"I think the first step went very well. We feel relieved. We are extremely happy," he said.
Detailed descriptions of the coitus were posted on the zoo's website, along with a picture and a 30-second video.
The video was aired on the main early evening news programme of public broadcaster NHK.
Public viewing was suspended last week when keepers noticed the pandas were in season, in the hope that they would have more luck reproducing away from the prying eyes of the thousands who visit the city zoo every day.
Shin Shin mated with Ri Ri in March last year and gave birth on 5 July - yielding the zoo's first giant panda cub in 24 years.
Announcements of the cub's subsequent death from pneumonia interrupted regular broadcasting, with the zoo's director making a tearful statement on the TV news.
Pandas, whose natural habitat lies in mountainous south-western China, have a notoriously low reproductive rate and are under pressure from factors such as habitat loss. China has about 1 600 pandas living in the wild.