Clarke birdied the 17th and 18th holes to finish his round of 3-under-par 69. He played bogey-free golf Thursday en route to a 6-under-par 66 on the West Course of Wentworth Club.
His 9-under-par 135 for 36 holes was one stroke better than Niclas Fasth of Sweden, who shot a 67 Friday.
"I played well again," Clarke said. "I had numerous chances everywhere and I'm pretty pleased with a 69. The wind was gusting and that's a pretty good score. I was hitting the edges on the hole all day and I am certainly playing well enough to be doing well in this tournament."
Clarke bogeyed the first and seventh holes but had birdies on Nos. 4, 12 and 13 before his late surge. But Clarke was not satisfied.
"My patience is being severely tested at the moment, severely tested," Clarke said. "I have to keep playing the way I have and hopefully my scores will get better."
Fasth, another member of Europe's victorious Ryder Cup team from 2002, had an even better finish, concluding with three straight birdies.
"It was a very undramatic round,' Fasth countered. "I just made my way around and made a few good shots."
This tournament also marked the return of Ernie Els, who was forced to sit out last week's Deutsche Bank Open due to a lingering wrist injury. The South African moved within three strokes of the lead after shooting a 69.