The Stormers sealed a last-gasp 28-26 Super Rugby win over the Blues at Eden Park on Friday.

Skipper Schalk Burger's late try capped a second-half comeback which saw the Stormers extend their lead in the South African conference and leapfrog the Crusaders into third spot behind the Blues and leaders Queensland Reds in the competition's overall standings.

Renowned for their muscular defence this season, the Stormers also showed attacking flair after trailing the Blues 19-3 at the break in a dramatic comeback, in which they scored three tries to their opponent's two.

With just two minutes to go, Burger powered over the line to level the scores and Dewaldt Duvenage's conversion sealed the win.

Burger said the victory in the second match of the Stormers' four-week Australasian tour showed the injury-hit team had learned from last week's loss to the Waikato Chiefs, when his team threw away a 20-3 half-time lead.

"It was important for us, at half time we were down and out," Burger said.

"We've lost 12-13 experienced players (but) after half-time we turned it around."

The Blues identified the Stormers' imposing rolling maul as a key element ahead of the game and lock Ali Williams contained the threat in the first 40 minutes, blunting the South Africans' attack.

The New Zealanders raced ahead in the first 40 minutes with four Luke McAlister penalties and a converted Alby Mathewson try, scored of the back of a jinking run from pivot Stephen Brett.

They appeared to have put the game beyond the Stormers' reach when Lachie Munro crossed the tryline just after the break.

But the Stormers changed tactics and kept the ball in hand for much of the second half, reaping rewards through tries by Juan de Jongh, Johann Sadie and Burger.

Burger's effort from a line-out drive in the 78th minute proved decisive. Referee Keith Brown sent it to the video match official, who ruled the Springboks stalwart had just forced the ball onto the chalk.

"I'm claiming it anyway," Burger said after the match.

For Blues captain Keven Mealamu it was a disappointing way to mark his 130th Super rugby game, a New Zealand record in the southern hemisphere competition.

"It was a tough game tonight, it's just disappointing we had a few tough calls that didn't go our way towards the end there," he said, blaming the loss on slipped tackles and "silly little errors".

"We should have done better," he said.

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