The defender deputised last season when Jones was injured and manager John Hughes confirmed the permanent appointment at an Easter Road press conference on Tuesday.
Hogg was signed from Ipswich Town by former Hibs boss Tony Mowbray just over four years ago.
Hogg said: "It is a great honour for me. I have been four and half years at the club and I know what it's all about.
"I feel part of the club and I hope to take it forward under the new management team.
"I feel the captain has to be the embodiment of a club so it is a big responsibilty."