Pietersen's try and another from winger Gio Aplon in the first half at the Forsyth Barr Stadium in Dunedin proved enough to give the Stormers a sixth win in six matches on their first foray outside South Africa this year.
The Highlanders, who had lost just one match this season to stand second in the standings behind the Stormers, showed plenty of endeavour but were unable to breach the Stormers' blanket defence and scored only through two Chris Noakes penalties.
"It definitely wasn't easy," Stormers skipper Jean de Villiers said in a pitchside interview. "It was against a quality side and we were probably a bit lucky with some tries in the first half but we'll definitely take the win."
With two of the meanest defences in the competition on display, points should have been at a premium and the Highlanders will have been disappointed with the soft try they conceded in the 13th minute.
Centre De Villiers twice hacked at a loose ball after a turnover and Aplon won a footrace with the Highlanders cover defence to touch down.
There was nothing soft about Pietersen's effort 20 minutes later.
The 27-year-old started the move with a searing 25-metre break from inside his 22 and finished it with a perfectly executed chip-and-chase over the head of the last defender for a converted try that gave the Stormers a 15-3 lead.
Peter Grant, who alternated the kicking duties with Pietersen, scored the only points of the second half with two penalties and the white-shirted defenders held firm against wave after wave of Highlander attacks.
The visitors survived the loss of hooker Tiaan Liebenberg to the sin bin for 10 of the last 14 minutes and fittingly it was Pietersen's tackle that denied the Highlanders a consolation try just before the siren by forcing centre Tamati Ellison to brush the touchline with his boot.
