The Irish Ryder Cup player took advantage of softer conditions on the West Course at Wentworth to move to 13-under 131, putting some distance between himself and Robert Karlsson and Miles Tunnicliff going into the weekend.
It was a great finish, a great back nine. I holed some great putts, McGinley said after making a 25-footer at the 10th, a 20-footer at the 13th, a 40-foot uphill putt at No. 15 and a 25-footer for eagle at the last.
Im not overconfident with the putter but I feel in control, said McGinley, who has changed his putting approach this year. Im rolling it well and its going in.
Karlsson birdied the last three holes for a 3-under 69 and a 135 total. Tunnicliff shot 65.
Oliver Wilson (66) shared the fourth spot with Soren Kjeldsen (65) and Marcus Fraser (69), five shots off the pace. Miguel-Angel Jimenez was another shot back after a 5-under 67.
The list of casualties included third-ranked Ernie Els, whose 73 for a 4-over total of 148 was three over the cut line. It was only the second time in 13 appearances that Els had missed the cut, the other coming in his debut year of 1992.
Colin Montgomerie also missed the cut for the first time since his first appearance in 1989. Montgomerie, playing here for the 20th consecutive year, shot 75 and was also 4-over.
You get what you deserve in this game, Montgomerie said. I didnt play well enough. I wasnt encouraged by anything today.
Montgomerie had three bogeys on the back nine, including on the last hole, where he chipped weakly and two-putted from seven feet.
Others who missed the cut were Justin Rose, who lost in a playoff last year, Darren Clarke, Jose Maria Olazabal and Michael Campbell.
Two-time U.S. Open champion Retief Goosen birdied five of the last seven holes for a 3-under 69, just slipping under the cut line.
Lee Westwood became the second big-name withdrawal when he pulled out with food poisoning after five holes. Vijay Singh withdrew before the event Thursday with a side muscle injury.
McGinley refused to get carried away by his position.
There are two long days ahead. But Im prepared for a long week, he said. Its a marathon and were only halfway through the marathon.
Karlsson played his approaches superbly at the last three holes. He hit a 9-iron to within one foot at the 16th, a sand wedge to within two feet at the 17th and a lob wedge to within a foot at the last.
The longest putt he holed was from six feet, after making three 25-footers Thursday.
But I hit a lot of very good putts between 10 and 20 feet and I dont know how some of them didnt go in. I actually putted better today, Karlsson said.
Wilson had a bogey-free round for his 66, which included an eagle at the par-5 fourth. He birdied the next and collected three more birdies on the back nine.
I played the par-5s well, hitting them all in two shots, said Wilson, who has three runner-up finishes this year. I need to start contending in these big tournaments. I feel good enough. The only thing missing is a win.