The Highlanders led 22-19 with five minutes to play but they failed to close the game out, making several handling errors and botching clearances to let the Lions off the hook and van Heerden made them pay.
He barged over from close range in the final minute to secure the win, their first at Carisbrook.
The crucial mistake came from young first five-eighth Lima Sopoaga, who did not find touch from a defensive penalty with 2min remaining, handing the ball to the Lions for one last -- and ultimately successful -- foray.
It was just the Lions' third win of the season, which sees them scrape off the bottom of the table, while the sixth-placed Highlanders' hopes of remaining in a playoffs position come weekend's end will hinge on other results. Their home match against the Force next week now becomes must-win.
Coming off a bye week, the Highlanders were rusty in the opening half and did not improve much in the second stanza.
The bottom-placed Lions fired the shots early on, displaying some physical prowess at the breakdown and forcing the home team into uncharacteristic mistakes -- notably not releasing at ruck time and making too many handling errors -- to take an early 6-3 lead.
The Highlanders took time to settle into the match, possibly feeling the effects of outstanding flanker Adam Thomson's late omission from the team because of ongoing rib problems, but when they did their response was decisive.
Sopoaga found second five-eighth Shaun Treeby with an inside pass from a scrum close to the line and the nuggety midfielder did the rest, running a superb line to split the defence and score his first Super rugby try.
Sopoaga added two more penalties to one from his opposite, Elton Jantjies, as the Highlanders took a 16-9 lead into the halftime break but the Lions played the more savvy rugby in the second half.
The hosts spurned two gift-wrapped penalty opportunities in a fruitless search of a try, a move that backfired when Lions No 8 Josh Strauss barged over from a quick tap close to the line to ensure the scores would be locked up at 16-16 heading into the final 25 minutes.
Both teams had counter-attack opportunities that they could not capitalise on and the game threatened to boil over in the final 20 as frustrations grew.
An all-in brawl even broke out, ensuring the Sanzar citing commissioner will earn his keep this week. Lions flanker Michael Rhodes was the catalyst, grabbing Highlanders wing Siale Piutau around the neck and flipping him over in a dangerous and ugly wrestling-style move that caused Piutau to unleash a punch to Rhodes' head.
Both players can probably expect a stint on the sidelines.
Sopoaga and Jantjies, who had a fine game with the boot, traded penalties before the Highlanders pivot kicked the go-ahead goal, but the Lions had the last laugh and celebrated as if they had won the competition after the video referee awarded van Heerden's try.
Lions 26 (Joshua Strauss, Wikus van Heerden tries Elton Jantjies 2 cons 4 pens) bt Highlanders 22 (Shaun Treeby try Lima Sopoaga con 5 pens) at Carisbrook Stadium. Referee: Jonathan White.
