Saturday's SPL result at Rugby Park set up an Old Firm title decider.
The Irishman finished at the second attempt just after the break before converting a penalty as Kilmarnock followed up their Scottish League Cup final win over Celtic.
Motherwell were lacking in creativity and missed the chance to move above Rangers into second place in the Scottish 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 on Sunday.
The victory proved a fitting tribute to absent Kilmarnock midfielder Liam Kelly, whose father's death had cut short their Hampden celebrations last Sunday.
Emotions remained mixed before kick-off. While warming up, the Kilmarnock players wore T-shirts with their grieving team-mate's name and number eight on the back with the message 'we are all with you' on the front.
Injured captain Manuel Pascali paraded the trophy to warm acclaim from both sets of supporters in the 6,878 crowd before the visiting team welcomed their opponents out with a guard of honour.
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.
Kilmarnock were without four of their cup final team in total with Mo Sissoko and Dean Shiels suspended and Danny Buijs injured. Lee Johnson and Dieter van Tornhout started after combining for the Hampden winner and defenders Zdenek Kroca and Lewis Toshney came in.
Motherwell brought back centre-backs Shaun Hutchinson and Tim Clancy following suspension and they dominated possession in the opening quarter.
Chris Humphrey put over several inviting balls from the right but Kilmarnock were sitting deep and making it difficult for the visitors - who lacked a spark up front - to break through.
The game opened up before the half-hour mark and home midfielder Gary Harkins became more influential.
Harkins opened up the visiting defence with the outside of his boot to set van Tornhout free, but Darren Randolph was quickly off his line to make the second touch his. Harkins was then given far too much space to shoot from 25 yards but Randolph got down to hold.
Killie created the best chance of the 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 drifted off Hutchinson's shoulder and collected James Fowler's through-ball. His first effort was blocked by Randolph but the ball came back out to him and his second shot deflected off the goalkeeper and evaded Hutchinson on the line.
Kilmarnock continued to get Harkins on the ball and he had a shot blocked by Randolph after nutmegging Jennings on a breakaway.
The Motherwell midfielder soon brought him down after he repeated the trick and Harkins curled the resulting free-kick just wide.
Heffernan doubled the advantage with a 61st-minute penalty. The trouble started for Motherwell when 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 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.
