The 32-year-old Spaniard, who had laser eye surgery last month to correct astigmatism, collected only four pars all day in a rollercoaster round at the Greg Norman-designed Earth course.
Garcia produced a flawless front nine containing five birdies and four pars.
He then played the inward half without a regulation figure, notching two eagles, four birdies, two bogeys and a triple bogey at the par-four 16th to finish with a seven-under aggregate of 137.
"I wish I could explain that," laughed Garcia. "Everything was going well until the 12th...and all of a sudden I kind of lost it a little bit.
"I missed a couple of short putts for par and then made a bomb on 14 for eagle before making a good birdie at the next hole," he told reporters on a sun-baked day at the European Tour's season-ending event.
"On 16 I probably hit the worst shot I hit all day. I just didn't commit to the shot I wanted to hit," he said referring to an eight-iron approach he dunked into water.
Garcia bounced back immediately with a birdie two at the 17th before "getting lucky" with his drive at the 18th where he grabbed his second eagle of the round.
"I hit the drive five yards left of where I wanted but got a very good bounce off the rocks and hit a very nice five-wood to 20 feet and holed a great putt from just off the green."
Garcia's 64 matched the previous record held by British pair Lee Westwood and Ross Fisher, Germany's Martin Kaymer, Peter Hanson of Sweden and defending champion Alvaro Quiros of Spain.
"I'm coming back from a long break so I'm trying to get some good vibrations going," said former world number two Garcia.
"I was trying to be as calm as possible because obviously I wasn't happy about my shot on 16. This is a course that if you drive the ball well, and I did today, you can make some birdies and eagles.
"I have had a couple of rounds before where I've hit a double-bogey mixed in with an eagle here or there but not like it happened on the back nine today."
Garcia, now down at 22nd in the world rankings, said he was still a long way from his best.
"I feel the rust from these last seven weeks without competing and I need to sharpen up," he added. "But it feels good to shoot a good round."
Overnight leader Luke Donald, who carded a 65 on the opening day, was a late starter on Friday.
"I'm expecting the leaders to finish somewhere around 11 or 12-under-par at least so I'll have to wait and see how far away I am," said Garcia.
The Spaniard said he had only noticed a slight improvement in his vision since the operation.
"Not immense but a little bit," he explained. "The main reason I had surgery was that I was feeling very uncomfortable with contact lenses.
"It was either do nothing or get the LASIK surgery and kind of get rid of it. I'm still getting used to it."