That put Wood 14 under, two ahead of Khan and Spanish star Sergio Garcia, who birdied the first, fourth and sixth.
“It's been a tough couple years since winning Wentworth, so it's amazing,” said Khan, who has had just one top-ten finish since holding off Luke Donald.
“The feelings start coming back pretty quickly in this game, which is good. Hopefully I can carry it on tomorrow.
“It was really good fun on the front nine, and I had a good up and down out of the waste area on three, which is a real tough one. I managed to par that and that really kept me going.
“I'm pleased with the back nine. I played quite nicely - left a couple of putts short but haven't been up there for a while, so hopefully I can do that a little bit better tomorrow.”
Runner-up in Abu Dhabi last weekend, Rose did then birdie the long tenth, but then came two bogeys in the next three.
Wood three-putted the 12th, but came back with further birdies at the 14th and 16th and matched Khan's 64.
At 15 under he was two in front of Garcia, who still had five to play, and three clear of Khan, New Zealander Michael Campbell and Swede Alex Noren.