Wilson had a great chance to win the game but his 35m penalty just shaved the left upright, and then he badly miscued a dropped goal attempt.
It is a cruel world, this Super 14. The Highlanders lost their seventh game out of eight but no-one would have begrudged them a famous victory.
Given no chance to topple the unbeaten Sharks, they had an inspired first 20min, scoring two fine tries, and finished with real desperation.
But handling errors and missed tackles blighted what was otherwise a fine performance by the Highlanders.
They are gallant losers, yet again, with a bonus point all they have to show for their efforts.
The Sharks flattered to deceive for much of the night but made a great start to the second spell when No 8 Ryan Kankowski, easily their best player, scored after just 80sec.
Kankowski swooped on an errant Toby Morland pass from a line-out and sprinted 50m to get the visitors' second try.
It was a pity Morland spoiled his night because he had been in splendid form in his first start of the season, passing swiftly and accurately and using his boot well.
The Sharks took the lead for the first time when Frans Steyn kicked a monster 53m penalty.
There was a real sense the Sharks were poised to break out of what, by their standards, had been a bit of a slump.
The Highlanders had plenty of opportunities to string something good together but they started to look a bit shaky and started to push and drop passes.
Steyn missed two penalty attempts, so the margin remained just two points for a good while.
Right to the end, in fact.
There was much excitement around the sparsely-populated ground when the Highlanders took something of a shock lead in the seventh minute.
Hoani MacDonald stole a Sharks line-out, the ball was spread at pace through the backs and Fetu'u Vainikolo - naturally - showed his great strength to get through four players and over the line.
That was Vainikolo's fifth try of his remarkable debut season. His power, pace and balance have made him the focal point of the backline every week, and all Highlanders fans will feel sore if this is his only season in the South.
The Sharks had been subdued, certainly for an unbeaten team travelling comfortably at the top of the table. And just when they started to show signs of waking up, the Highlanders struck again.
It was simple stuff, too. A good attacking scrum was set, Vainikolo attacked the line, Craig Newby had a go, and finally big prop Clint Newland crashed over.
The Sharks have built their success on a close to impenetrable defensive line but the Highlanders showed real flair in breaching it twice in 20min.
There was a hint of excitement in the air - yes, excitement at Carisbrook, imagine that - as the game opened up.
There were just two problems for the Highlanders: their line-out was just this side of terrible, and they were missing a swag of tackles.
One of the misses hurt them at the tail end of the first half when the Sharks broke down the left and Chris King was responsible for a bad miss that let Jacques Botes in for a try.
A well-struck Wilson penalty late in the half had the game firmly in the balance at halftime.
The Highlanders fly to Africa this morning, bound for games against the Bulls, the Stormers and the Cheetahs that will be a thorough test of their spirit.
Sharks 19 (Jacques Botes, Ryan Kankowski tries; Ruan Pienaar 3 penalties), Highlanders 17 (Fetu'u Vainikolo, Clint Newland tries; James Wilson 2 conversions, penalty). Half-time: 11- 17. Referee: Ian Smith (Australia). Crowd: About 6000.
