Biggio was in the lineup, batting eighth and playing second base, the position where his father won four Gold Glove awards playing for Houston. The elder Biggio was in Toronto to attend his son's debut.
The younger Biggio went 0 for 3 and struck out twice as the Blue Jays lost 6-3 to the Padres.
Toronto last month gave a debut to the son of a Hall of Famer, and third baseman Vladimir Guerrero Jr. has become a regular starter. Among the Blue Jays top minor league prospects is Bo Bichette, whose father Dante played in the majors.
A fifth-round pick in the 2016 amateur draft, Cavan Biggio hit .307 with six homers and 26 RBIs in 42 games at Triple-A.
Biggio was one of four players to join the Blue Jays on Friday. Toronto recalled infielder/outfielder Lourdes Gurriel Jr., and left-hander Thomas Pannone from Triple-A, and added lefty Zac Rosscup, who was claimed on waivers from Seattle on Thursday.
Biggio's contract was selected from Buffalo of the International League, and outfielder Billy McKinney and infielder Richard Ureña were optioned to Triple-A. Left-handed knuckleballer Ryan Feirabend was designated for assignment and right-hander Elvis Luciano was placed on the bereavement list.
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