After beating the Bulls last week the Blues faced a tall order after trailing the Stormers 24-3 early in the second half.
Tries from Benson Stanley and Charlie Faumuina closed the gap to seven with 15 minutes remaining however a late Stormers penalty closed out any chance of a comeback.
The Stormers had plenty of help from their star backline duo Jean de Villiers and Bryan Habana with both crossing over for tries to give the home side a handy 21 point lead.
The Blues showed strength to get back into the match but ultimately came away with nothing after being denied any bonus points.
The defeat is the Blues' third of the season and leaves them at the bottom of the New Zealand conference as they head back home to host the Hurricanes next Friday.
The win lifts the unbeaten Stormers to the top of the overall standings with 16 points, two points ahead of the Chiefs, who have played an extra game.
Blues captain Keven Mealamu said in the post-match interview that the first half deficit was too much for his side.
"The Stormers came out strong from the first whistle, we needed to come away with more points from that first half because we worked hard in that second half and were able to get ourselves back in the game. But it was a tough mountain to climb with so many points to collate in that second half."
- Cameron McMillan
