The former "30 Rock" star and the yoga instructor announced their son's arrival via their social media accounts by sharing a picture of a baby's hand clutching a finger, reported New York Daily News.
"We are happy to announce the birth of Rafael Thomas Baldwin," Alec posted on twitter.
The couple married in 2012 and welcomed their daughter Carmen in 2013.
Alec, 57, also has a 19-year-old daughter, Ireland, with his ex-wife, actress Kim Basinger.