The Waratahs ran in 11 tries in a record win over the Southern Kings last week but against the Stormers' miserly defence had to be satisfied with scores from winger Cam Crawford in the first half and fullback Folau's late effort.
Five kicks from five attempts by Stormers fullback Joe Pietersen meant the Waratahs trailed 15-11 until Folau managed to breach the line, further pressing his claims for a place in the Wallabies squad for the British and Irish Lions tour.
Replacement flyhalf Berrick Barnes, playing only his second match of an injury-ravaged season, provided the pass that allowed Folau to score, converted the try and kicked a penalty from halfway as the clock ran out.
"I'm more pleased than last week to be honest," said Waratahs skipper Dave Dennis, whose side still have a chance of making the playoffs and host Australian front-runners the ACT Brumbies next week.
"We just want to keep this winning feeling going next week hopefully."
Folau's most telling contribution in the first half owed as much to his rugby league background as his newly learned union skills, leaping up to knock back a Bernard Foley crosskick for Crawford to touch down in the 24th minute.
Both defences held firm at the gainline and it was not until the stroke of halftime that Brendan McKibbin was able to extend the lead to 8-3 when the Stormers were penalised for the sixth time.
Early in the second half it was the home side's turn to attract the ire of referee Chris Pollock, who will officiate one of the Lions tests, and Pietersen converted two penalties in four minutes to put the visitors in front.
McKibbin's second penalty put the Waratahs back ahead after 50 minutes but Pietersen made no mistake with two further efforts to put the Stormers 15-11 ahead with 15 minutes to play.
It looked for most of that time that the Stormers would hold on but the Waratahs held their nerve and were rewarded with Folau's try after a long siege of the visitors' line.
Springboks number eight Duane Vermeulen left the field 10 minutes from time after sustaining what looked like a serious knee injury and Stormers skipper Jean de Villiers said that had disrupted their defensive effort.
"We fought back nicely to get the lead but ... then we gave up the try and we couldn't hang onto the ball," he said.