The actor's friend, director Viktor Kossakovsky announced the news at Zurich Film Festival - as the Joker star had been due to attend to promote their new film Gunda.
The newborn's name is a tribute to Joaquin's brother, River Phoenix, who died aged 23 in 1993.
Neither Phoenix or Mara have much of a presence on social media, but Kossakovsky confirmed that during lockdown they had a child together.
The couple met and started dating after working together on the 2013 film, Her.
Because of the impact of the global pandemic, the director said Phoenix will now start promoting the movie Gunda in the US, in his role as executive producer.
🚨 Viktor Kossakovsky 📽️, Gunda: He just had a baby Boy who's Called River. ( about Joaquin) pic.twitter.com/WuUISnuTsZ
— JOBSTERS IT (@Paula_FlorV) September 27, 2020
