The former Ryder Cup star, who is in contention for the captaincy of the 2014 team, showed a touch of the old magic as he cruised around in a seven-under-par 65.
Out in 33, back in 32, five birdies and an eagle three on the 577-yard par-five 16th -- yer man McGinley made golf look ridiculously easy.
The 45-year-old Dubliner, currently 69th in the Race to Dubai rankings and No 322 in the world, was delighted with his performance and his strong finish.
He holed from 30 feet for his eagle on 16, took a solid par-three on 17, and then almost holed his approach to the difficult 456-yard last hole.
"It turned a good day into a great day. In all my life I don't think I've been on that 16th in two before -- that's new technology for you," he said.
McGinley's 65 left him tied for third alongside England's Danny Willett and Chris Wood. The trio were a shot adrift of joint leaders Marcus Fraser ( Australia) and Fabrizio Zanotti (Paraguay), who each carded 64.
Colin Montgomerie, back from television commentary work in San Francisco, shot 69, but local favourite Martin Kaymer struggled with jet-lag -- "I slept for only two hours," he said -- and had to settle for a 71, the same as Sergio Garcia.
The standard of golf and the vulnerability of the course was such that unless competitors were scoring birdies, they were sliding down the leaderboard, and the rest of the Irish need to be focused today if they are to make the cut.
Harrington started well, with birdies on the first two holes, but he had a double-bogey six on the fourth and a bogey four on the par-three fifth. He bounced back with a birdie three on the sixth and finished the first nine on a level-par 35.
Meanwhile, Alan Dunbar defied winter-like conditions to move into the quarter-finals of the Amateur Championship at Royal Troon yesterday.
The 22-year-old Walker Cup man from Rathmore was awesome in demolishing Denmark's Patrick Winther 7&6 but then had to pull out all the stops to get past Frenchman Paul Barjon on the home green.
Dunbar came to the last one up and settled the issue in clinical style with a birdie. He now faces Sweden's Robert Karlsson for a spot in the last four.
Headfort's Rory McNamara got off to a fast start against German Stephan Jaeger winning the first four holes and went onto win 4&3 in round three, but despite a promising start, Scotland's Jack McDonald ended his involvement.
Kevin Phelan,the Waterford Castle golfer who lives in Florida, went down in the third round on the 19th hole to Italian Lorenzo Scotto.
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