The Stormers won for the first time in five matches and dealt a major blow to the Blues' Super Rugby hopes by winning 30-22 in Cape Town on Friday.
Tries from Siya Kolisi, Dillyn Leyds and Sikhumbuzo Notshe secured the victory for the leaders of the Africa 1 conference, while the Blues now find themselves cast adrift at the bottom of the New Zealand standings.
After conceding an early penalty and losing Matt Duffie to a yellow card for persistent fouling, the Blues survived a Stormers siege to open the scoring through George Moala, who benefited from Charlie Faumuina's quick hands to cross at close range, Piers Francis converting.
That try arrived just after Eben Etzebeth, back in the team after recovering from a minor injury, had seen yellow for his role in a big melee near the Stormers' try line.
Faumuina's clever floated pass allowed captain James Parsons to cross in the corner for the Blues' second with seven minutes to go in the half.
There was still time, though, for Kolisi to barge his way over following a scrum and SP Marais to convert, making it 12-10 in the visitors' favour at the break.
Sonny Bill Williams was the architect of the Blues' third try, his pick and drive leading to Blake Gibson crossing four minutes into the second half.
Francis added the extras but quickly found himself out of the game, suffering a suspected concussion after a high, swinging tackle by Shaun Treeby, who was fortunate to escape the sin bin.
The Blues responded well, applying consistent pressure and finally hitting back through Leyds, who caught his own chipped kick to score in the 61st minute. Marais, having earlier sent over a penalty goal, added the extras to put the hosts back in front.
After Kara Pryor stopped Cheslin Kolbe with a try-saving tackle on the wing, Duffie earned his second yellow for a clumsy follow-up tackle on the prone Stormers player.
Substitute Notshe was awarded a try in the 70th minute after escaping a review from the television match official for a suspected double movement, Marais converting to extend the home team's advantage.
Francis' replacement Bryn Gatland sent over a penalty from 40 metres out to close the gap to five points with six minutes to go, but Marais returned fire to afford the Stormers a measure of comfort in the final minutes.