The baby was born in June, reported People magazine.
McCauley and Gordon-Levitt, 36, share another son, who turns two next month.
A representative had confirmed the news of Gordon-Levitt and McCauley's second child on the way in May.
The actor and the businesswoman have kept most aspects of their relationship out of the public eye. The duo quietly tied the knot at their home in December 2014, and in the beginning stages of their relationship, Gordon-Levitt wouldn't publicly name his then-girlfriend.