A red card to Blues lock Hayden Triggs for punching Stormers No 8 Duane Vermeulen in the face in the first half meant this match was as good as won by the home side at halftime.
That they failed to score a try after the break - the Blues scoring some sort of victory by winning the second half 10-9 - owed much to the Stormers' lack of composure on attack but probably more to the Blues' commitment on defence and everywhere else.
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The loss of Steven Luatua in the first half with what appeared to be a shoulder injury also hurt.
Jerome Kaino got the better of his opposite No8 and skipper Vermeulen, who was celebrating his 100th Super Rugby match, and Brendon O'Connor and Luatua's replacement Luke Braid tackled and scrambled and made life extremely difficult for the Stormers at Newlands in Cape Town.
Braid went over the try line after a break by Charles Piutau, easily the Blues' most dangerous attacking threat, electing to pass to Jimmy Cowan in order to make Ihaia West's conversion easier. It drew the Blues closer to 21-16 and the nerves started showing from the Stormers, who would have been aware of the Sharks' escape act when winning in Christchurch against the Crusaders with 14 men last year, but a constant stream of penalties by the Blues let them off the hook.
"Once we got the card we knew we had to dig deep," Kaino said afterwards. "We hung in tough in the first half but in the second half the ill discipline really cost us.
"The ref made his decision and we couldn't really argue with it," he said of Craig Joubert's decision to send Triggs off. "We just had to rally with everything we had."
There was some silly stuff from the Blues, apart from Triggs' obvious brain explosion in connecting with Vermeulen twice with his fists after 24 minutes. But there was also some clever thinking. Twice they neutralised the Stormers' lineout drive only metres from their line when standing off without engaging, earning a scrum feed from Joubert.
The scrum wobbled a couple of times, but despite Kaino going to lock and them having wings Ben Lam or Tevita Li hanging on at blindside flanker, the Blues were not embarrassed.
Their lack of attacking thrust - Piutau apart - remains a concern, as does their table position of second to last, but the Blues will head to Bloemfontein and the Cheetahs confident of making amends after their two defeats.
Stormers 27 (Nic Groom, Dillyn Leyds tries; Demetri Catrakilis con, 4 pens; Kurt Coleman pen)
Blues 16 (Jimmy Cowan try; Ihaia West con, 3 pens)