Melbourne Victory striker Archie Thompson pinched a winner deep in injury-time to secure a pulsating 2-1 A-League derby triumph over crosstown rivals Melbourne Heart at AAMI Park on Saturday night.

Thompson netted via the crossbar two minutes into injury time to snatch all three points and sink the Heart, who had grabbed an equaliser just minutes earlier.

The win lifts the Victory to third place and leaves the Heart third from bottom.

Victory took the lead with Marco Rojas' 67th-minute goal - a wonderfully-worked move sweeping through Thompson, Gui Finkler and Mark Milligan before the New Zealander finished sweetly.

But the Heart looked to have earned a share of the points when skipper Fred, who had missed his side's two best chances of the match earlier, leapt high to meet a superb Michael Marrone cross and finish.

Then the Heart lost possession in the middle of the park in injury time.

Rojas grabbed the ball and sent a slide-rule pass to Thompson, whose shot hit the crossbar and crept just inside before Heart defender Aziz Behich thumped it out in vain.

With more than 26,000 watching on, it was a first half of desperate defence - four shots blocked, cleared off the line or deflected to safety in a spirited opening 45 minutes.

Fred had the Heart's two best chances, squandering a first-half opportunity on 32 minutes when he shot dreadfully from Behich's superb run to the byline and cross.

But he went within a coat of paint of a spectacular goal six minutes after halftime, controlling then thumping a wonderful long-range volley just wide of the top corner.

- AAP