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It was an unconvincing victory in front of a sell-out 80 000 crowd, but ensured the Socceroos will appear at their third consecutive World Cup, alongside Japan who are already through from Asian Group B qualifying.
The result put Australia on 13 points, out of reach of Oman (nine points) and Jordan (seven points) who play later Wednesday.
Australia wasted countless chances in wet conditions before coach Holger Osieck replaced a visibly angry Tim Cahill with Kennedy in the 77th minute.
But the towering Nagoya Grampus striker justified the substitution when he saved the day with a clinical 83rd-minute header that sent the crowd wild.
"I'm proud of everybody. It's been a really hard campaign but we showed our mental strength," captain Lucas Neill said. "I'm sorry it wasn't pretty but we beat them.
"We've got to keep pushing ourselves," he added. "Let's look at the positives tonight -- we're going to Brazil!"
Osieck kept his faith in the team that impressively beat Jordan 4-0 in Melbourne last week and they repaid the German, but it was not the authoritative performance that many were expecting.
He was relieved that his team scrambled over the line.
"It was a very tough qualifying campaign but we made it happen over the last three games," said Osieck. "I'm simply happy for the boys and the fans. It was a tricky game, they are tough to play."
Former Asian champions Iraqi had no chance of qualifying for Brazil and were without veteran skipper Younis Mahmoud and midfield maestro Nashat Akram, who opted not to play.
Attacking midfielder Alaa Abdul-Zahra was also absent with the team predominantly made up of players who will compete at the Under-20 World Cup in Turkey later in June.
Their inexperience showed and they were immediately on the back foot with a left-foot strike by Cahill in the second minute forcing a fine save from Noor Sabri, one of only two survivors from Iraq's 2007 Asian Cup-winning team.
Sasa Ognenovski went close 12 minutes later when he got his head on a Lucas Neill cross as the Socceroos made good use of space on the wings, and Cahill leapt well to get a header on target from a Luke Wilkshire corner soon after.
Half-an-hour in and goalkeeper Mark Schwarzer had barely touched the ball as Australia pressed for the opening goal.
Cahill again went close, twice in as many minutes, but the killer strike eluded them and they went into half-time at 0-0.
Iraq had their first shot on target soon after the restart when Saif Salman forced Schwarzer into action as Vladimir Petrovic's team upped the tempo.
Australia responded and thought they'd scored after 64 minutes when Robbie Kruse volleyed the ball into the net, but the referee had already blown for a foul in the penalty area.
With the game heading for a draw, Osieck brought on Kennedy and despite Cahill petulantly swiping the air close to the coach's head, the move paid dividends.
As the clocked ticked down Mark Bresciano looped in a cross from the right and the lanky Kennedy made no mistake, climbing to meet the ball and heading it into the right-hand corner.
Reaching Brazil is a dream come true for the Socceroos, many of whom are 30-plus and will have their last chance to play in a World Cup in 2014.
Australia's
most capped player Mark Schwarzer will be 41 come next year's
showpiece, while captain Lucas Neill, striker Tim Cahill and midfielder
Mark Bresciano will all be 34 or older.
