Heffernan took less than three minutes of his first competitive start to get off the mark when he slid the ball home from 12 yards after Rory McKeown's ball over the top in Sunday's SPL clash at Rugby Park.
The Irishman finished the scoring with 20 minutes left when his cushioned volley found the top corner after James Dayton had sent Danny Buijs down the right.
Heffernan should have scored at least one more - he hit the bar from six yards after substitutes Jorge Galan and Dean Shiels had taken the Hibs defence and goalkeeper Graham Stack out of the equation.
He also went close in the first half when a brilliant through-ball from Gary Harkins split the youthful Hibs defence, Stack recovering to save after the 29-year-old had taken the ball round him.
Shiels felt the end product was the only thing missing from Kilmarnock's previous SPL games, draws against Dundee United and Motherwell.
Shiels said: "It's brilliant for Heffernan. We worked on that all week to try to give him a better supply.
"I felt we weren't early enough to his movement, we worked on that and got results."
But Shiels added: "The one he hit the bar, I don't know, I think my granny would have scored that one. I think he thought he was back for a corner kick."
The victory was Shiels' first as manager at the 11th attempt and Heffernan was just as happy for his boss, who never wavered from his demand for passing football.
"He is absolutely adamant that's the way he wants to play," Heffernan said. "You have to respect him for that.
"At Doncaster [one of his former clubs] we were known for passing the ball but I have not known it to this extent - the goalkeeper is not allowed to kick it long.
"I found it a bit hard to adjust in pre-season. I found I wasn't seeing a lot of the ball as the team passed it around behind me, but the manager and Jimmy Nicholl just told me to be patient and play on the last defender and the chances will come."
Hibs striker Garry O'Connor levelled in the 13th minute with a brilliantly-taken goal but there was little else to cheer manager Colin Calderwood.
His side looked a beaten team after James Dayton curled the third from a 25-yard free-kick.
But Calderwood said: "There is nothing to worry about, it is just normal practice, you go to work.
"Too many had a bad day and that accumulated. We didn't play well but we were competitive until the third goal.
"The last half hour was hurtful to watch and I understand that, but I think it's a terrific lesson."