Play was suspended on Friday afternoon as winds reached 36mph and blew trees over at Emirates Golf Club.
Garcia, who was eight under after five holes when play was stopped, added five birdies and a bogey as he carded a five-under-par 67 to move 12 under.
Nacho Elvira is nine under, a shot clear of Open champion Henrik Stenson.
England's Chris Paisley carded the joint-best second round with 66 as he completed 14 holes in the better conditions to sit tied for fifth on seven under.
"Obviously we got a bit lucky with the weather today. I was expecting it to be windier, but you still have to hit good shots," said Garcia, who is looking for his first European Tour win since 2014.
"I played nicely again and made some nice putts, so I'm very happy with where I am."
The third round is under way with plans to try and complete it on Saturday.
Spain's Sergio Garcia opened up a three-shot lead in the Dubai Desert Classic as the delayed second round was completed on Saturday morning.