Flyhalf Morne Steyn kicked 20 points and wing Francois Hougaard broke clear for a first-half try as the defending champions from Pretoria led from start to finish.
Bryan Habana, who helped the Bulls clinch their first title in 2007 and won with them last year, raised hopes of a Stormers recovery with his 54th-minute intercept try - his third in two weeks against his former team.
Replacement scrumhalf Ricky Januarie stretched over late for the Stormers as the Cape Town team outscored the Bulls two tries to one but ran out of time.
Steyn landed seven from eight kicks at goal to lead the Bulls to victory in the last Super 14. The Melbourne Rebels join an expanded Super 15 next year.
South Africa President Jacob Zuma appeared on the field before kickoff and told the sellout 40,000-strong crowd he delayed an international trip to be at the final, which he called a significant moment in the history of South Africa.
The Bulls - whose own stadium is in the control of FIFA for the football World Cup - were playing for the second time in the famous black township on the outskirts of Johannesburg.
Backed by the majority of the crowd, who adopted football fans' vuvuzela trumpets for the game, the Bulls never trailed.
Springboks No. 10 Steyn kicked two early penalties to increase his record points haul in a Super 14 season to 249. With 13 former winners in their side, the Bulls hogged possession and dominated territory in the opening stages.
Trailing 6-0, the Stormers, second to the Bulls in the regular season standings, were denied a 19th-minute try when captain Schalk Burger reached out for the line at the bottom of a ruck. The television match official ruled out the score.
Steyn extended the Bulls' lead just a minute later with a long-range penalty after the Stormers were penalized near the halfway line.
Hougaard then put the Bulls in complete command as he broke through a gap on the edge of a ruck and stepped past Stormers fullback Joe Pietersen for the game's only try of the first half.
The Bulls had shrugged off the loss to injury of leading tryscorer Gerhard van den Heever inside 10 minutes.
The Stormers, however, struggled to reproduce their regular season form and had to wait 30 minutes for their first points - a Peter Grant penalty when Bulls lock Danie Rossouw was penalized by referee Craig Joubert.
Grant was met with a deafening blast of noise from the Bulls fans' vuvuzelas as he lined up the kick.
Grant missed a penalty from near the touchline early in the second half but Habana intercepted a Steyn pass soon after and sprinted clear to boost the Stormers' hopes as they closed the gap to 16-10.
The Bulls took control of the ball again, and Steyn fired over another three penalties to take the champions out of reach.
Januarie crawled over with three minutes to play as the Stormers lifted themselves for one final effort.
But the Bulls closed out the final to claim their third Super 14 title in just the second all-South African final in Super rugby history.
The southern hemisphere's strongest team over the last four years will keep the trophy after winning it for a third time.
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Bulls 25 (Francois Hougaard try; Morne Steyn conversion, 6 penalties), Stormers 17 (Bryan Habana, Ricky Januarie tries; Peter Grant 2 conversions, penalty). HT: 16-3.
