Irishman Shane Lowry finished alone in second on eight under par after notching seven birdies in his final-round 66.
The 31 year old had given Garcia a scare when he closed the gap to a single shot courtesy of three birdies in a row at the start of the back nine but a disappointing double bogey at the short 15th derailed his challenge.
Finn Mikko Korhonen was another two shots back in third, one ahead of Ashley Chesters in fourth, with seven-time European Tour winner Gonzalo Fernández-Castaño finishing in the group in a share of fifth on four under to jump into the top 116 in the Race to Dubai Rankings presented by Rolex and retain his playing privileges.
Scot Richie Ramsay also kept his card after finishing in a share of 11th on two under par to jump up to 115th on the list, with David Horsey clinching the final place.
Garcia had opened his final round with a birdie and one bogey in his first seven holes to remain at ten under par before the hooter sounded at 1.49pm on Sunday.
And with the threat of lightning keeping the players off the course for the rest of the day, it was announced the last full-field event of the European Tour season would run into a fifth day.
When the action resumed at 9.10am local time, Garcia safely parred the final two holes of his front nine to reach the turn in 35 and maintain his three-stroke advantage on ten under par.
A birdie from around nine feet at the tenth took Garcia to 11 under and handed him a four-shot lead.
It's amazing to be able to win here at Valderrama three times - it's a dream come true - Sergio Garcia
But a bogey on the 13th and a birdie burst from the charging Lowry saw Garcia's lead shrink to one stroke with five holes of his round remaining.
Europe's leading Ryder Cup points scorer bounced back with a birdie at the 14th and when Lowry put a double bogey on his card at the 15th, Garcia's advantage was back to four shots.
After Lowry had closed his round with a birdie three at the 18th, Garcia picked up a shot at the 17th to get to 12 under and claim the title.
Garcia called winning for the third time at Valderrama a "dream come true".
He said: "It's amazing to be able to win here at Valderrama three times - it's a dream come true.
"It's so difficult. This golf course is so challenging and for me to be able to go out there in the conditions we played in all week and shoot three rounds under par means a lot. I'm very proud of that and really excited about the week.
"I knew the guys were going to be going after me and this golf course is the kind of course where if you're a little bit off you can struggle.
"But if your game is on it gives you a lot of birdie opportunities.
"And obviously Shane was playing well - he got close to me - then unfortunately he doubled 15 and that gave me a little bit of an extra gap, with his double and my birdie on 14 opening it to four, and we kept it there until the end so that was nice."
After securing his best finish of the season so far, Lowry said: "I was going well yesterday but I came back out this morning on fire as well and birdied ten, 11 and 12, lipped out on 13 and 14 and then hit the worst shot I’ve hit all year on 15 and made a double there.
"But the positive is that it’s probably the only bad shot I hit in that round.
"A 66 around here and being in contention is pretty good. I’m just disappointed I didn’t put a bit of pressure on Sergio. I had it to within one at one stage and then I made double and he made birdie. That was it.
"But it’s my best week of the year - there are serious positives to take from it, and I’ve got a great four weeks coming up now to finish the season."