Heffernan scored 27 goals in 61 appearances in two seasons at Kilmarnock but manager Allan Johnston has decided he has enough up front with Kris Boyd, Mark Stewart and William Gros.
The 31-year-old Irishman, who has played for the likes of Doncaster and Sheffield Wednesday, has signed a contract until the end of the 2014/15 season.
Heffernan told Hibernian's official website: "I'm excited about starting the next chapter of my career at Hibernian; hopefully my time with the club will be successful.
"I spoke to both Michael (Nelson) and Tim (Clancy) about coming here and they both encouraged me to join.
"It's a good club with big support - I saw that at the cup tie at Rugby Park last season - and I'm looking forward to playing for Hibs."
Manager Pat Fenlon has now signed 10 players this summer, with Heffernan competing with fellow new recruits James Collins and Rowan Vine for a place up front.
Fenlon said: "We're delighted to be able to get Paul - the situation concerning his arrival developed very late on.
"He is a good, experienced player and his goalscoring record is very good. He knows the league inside out and he's different to what we have.
"Paul comes in with a good pedigree and hopefully he will bring both goals and experience to the team."
Fenlon's other signing, 21-year-old Zoubir, joins from Ligue 2 side FC Istres on loan for the season following a successful trial this week, subject to international clearance.
Fenlon also took Ipswich winger Josh Carson on trial this week after losing Alex Harris and Paul Cairney to injury but his summer business looks to be done.