El Hadary, the Egypt captain who turned 44 on Sunday, was not named in the Pharaohs' starting line-up for their Group D opener against Mali.
However, he was introduced as a 25th-minute substitute after Ahmed El Shennawy was forced off injured.
El Hadary - a four-time winner of the tournament - beats the previous mark set by his fellow Egyptian Hossam Hassan, who was a mere 39 years, five months and 24 days old when he played at the 2006 Cup of Nations.