The Irishman finished at the second attempt just after the break before converting a penalty as Kilmarnock followed up their shock Scottish Communities League Cup final win over Celtic.
Motherwell were lacking in creativity and missed the chance to move above Rangers into second place in the Clydesdale Bank Premier League. They now find themselves too far behind Celtic to deprive the leaders of a title party should Neil Lennon's men win at Ibrox .
The victory proved a fitting tribute to absent Kilmarnock midfielder Liam Kelly, whose father's death had cut short their Hampden celebrations last Sunday. With the cup sitting in the centre circle, a minute's silence was held for Jack Kelly, who died aged 59 after collapsing in the Hampden stand moments after the final whistle.
Killie created the best chance of the first half in injury-time when Heffernan ran across the Motherwell central defence and took Garry Hay's pass - but he shot inches wide of the far post.
The hosts maintained the pressure after the interval and Heffernan profited from some more clever movement in the 50th minute. The striker collected James Fowler's through-ball and after his first effort was blocked, the ball came back out to him and his second shot deflected off the goalkeeper and evaded Shaun Hutchinson on the line.
Heffernan doubled the advantage with a 61st-minute penalty. The trouble started for Motherwell when Steve Jennings found himself under pressure in his own half and passed to Hutchinson, who was immediately tackled by James Fowler.
With Motherwell exposed, Fowler's shot was charged down and Tom Hateley blocked with his hands as he slid in to close down Hay. Referee Crawford Allan pointed to the spot and Heffernan put his penalty just out of reach of keeper Darren Randolph and into the corner of the net.
Well manager Stuart McCall transformed his attack midway through the half with Bob McHugh, Jamie Murphy and Omar Daley on for Nicky Law, Henrik Ojamaa and Michael Higdon.
But the visitors remained short on imagination and they were again caught out after losing the ball in their own half with young substitute Chris Johnston, on for his debut, seeing two shots blocked.
Goals from Johnny Russell and Gary Mackay-Steven extended
Gregory Tade's first-half strike gave 10-man
Jim Jefferies had to be happy with a point in his first game as