Jean-Matteo Bahoya gave Frankfurt the lead in the 10th minute on Sunday following a neat triangle with Hugo Ekitike and Fares Chaibi.
The hosts then increased their lead in the 42nd, this time with Ekitike serving defender Robin Koch, who finished like a striker to find the bottom right corner.
Ekitike also got his name on the scoresheet as he finished into the open net from close range in the 71st minute to put the game to bed.
Frankfurt remained third and three points ahead of fourth-placed RB Leipzig. Heidenheim, meanwhile, are 16th and the first team in the drop zone.
In the day's other game, striker Oliver Burke completed a brace in the 90th minute to give Werder Bremen a 2-1 win at 10-man VfB Stuttgart.
Hosts Stuttgart had taken the lead in the 19th through Leonidas Stergiou, but Bremen were level in the 32nd after racing back upfield from a Stuttgart goal-kick. Mitchell Weiser emerged with the ball and found Burke, who side-footed the equalizer into the net.
Stuttgart's hopes of a win took a huge blow in the 65th as Nick Woltemade was sent off after a second yellow card.
Goalkeeper Alexander Nubel made a big save in the 83rd to deny Bremen a winner as the hosts thought they would snatch at least a point.
But there was nothing the Germany keeper could do to stop Burke from completing his brace and claiming all three points for the guests.
On Saturday, leaders Bayern Munich had to settle for a 2-2 draw with Borussia Dortmund, while champions Bayer Leverkusen were held to a goalless draw by Union Berlin.
Bayern top the table six points ahead of Leverkusen with five games left.
