John, 65, said on his website Tuesday baby Elijah Joseph Daniel Furnish-John was born Jan. 11.
The Johns are also parents to 2-year-old Zachary.
"Both of us have longed to have children, but the reality that we now have two sons is almost unbelievable. The birth of our second son completes our family in a most precious and perfect way. It is difficult to fully express how we are feeling at this time; we are just overwhelmed with happiness and excitement," the couple said in a statement to Hello! magazine.
Elton John married David Furnish, 50, in 2005 after 12 years of dating.