Kenny Shiels named Heffernan among his substitutes for the match as the Killie manager kept his faith with Mark O'Hara, William Gros and Ross Barbour after his youngsters impressed in the midweek defeat at Celtic Park.
But Heffernan stole the show when drilled home to break the deadlock just before the hour and flicked home Barbour's strike with five minutes left to condemn Caley Thistle to their third defeat in a week.
Nicholl said: "We knew it was going to be difficult because of the way they have been this season and what we had on the park, with the inexperience.
"The manager had a decision to make and it turned out to be the right decision to stick with the young lads, Barbour and Gros and O'Hara.
"They did really well. I thought Willie Gros was excellent up front, O'Hara's composure, and Barbour's willingness, and then the attitude of the senior players who might have been disappointed they didn't start.
"Heffernan got two goals coming on and showing a wee bit of composure, and everything went right for us on the day.
"It just shows you how substitutions go for you accidentally and it has worked out for Heffernan today, but there is no getting away from his composure for the first one and his quick-thinking for the other one."