The Sky Blues will host Brisbane Roar in the next round after James Donachie and Harry Van Der Saag's late efforts on Wednesday proved enough to end the Bulls' maiden Cup run.

"There was a lot of positives out of the game," Sydney coach Steve Corica said.

"We saw the game out, we finished very strong, which is a good sign as well, that our fitness is really good."

In a game initially delayed half-an-hour by bad weather, it took 100 minutes for either team to break through at Netstrata Jubilee Stadium.

Centre-back James Donachie proved the unlikely hero after regular time.

With scores locked at 0-0, midfielder Anthony Caceres played a one-two with Paulo Retre then put in a teasing ball to the back of the six-yard box, where Donachie rose highest to score a looping header.

A minute later, Macarthur's Andonis Martis received his marching orders for a challenge on Sydney striker Adam Le Fondre.

Sydney made their numbers advantage count in the 118th minute.

Van Der Saag, deputising for the absent Rhyan Grant, got through on goal and coolly dinked the ball over Macarthur goalkeeper Filip Kurto to seal the result.

Earlier, Le Fondre had the ball in the back of the net in the 83rd minute but was ruled offside, while Kurto previously thwarted chances from Retre and Max Burgess.

"Today gave me an indication of what kind of depth we have at this football club," Macarthur coach Ante Milicic said.

"I go home tonight definitely disappointed with the result but at the same time there's a few players, without mentioning names, that we know we can count on moving forward."

Australian Associated Press