McIlroy was just five shots off the clubhouse lead when he finished his round, but ended the day nine adrift of former Open champion Louis Oosthuizen and American Kyle Stanley.
A day after making a hole-in-one on the 17th hole and its island green in the opening round of the Players Championship, the 37-year-old Spaniard saw his tee shot on the par 3 hit the bulkhead, bounce in the air and land safely on the green before two-putting from 46 feet for par.
Making his first start since claiming a maiden major title at Augusta National, Garcia had been four over par for his first six holes at Sawgrass after four-putting the fifth, the same hole he six-putted in the third round a year ago.
After Pat Perez showed the field a low score could be had after he posted a best-of-the-day 66, Garcia made a significant move up the leaderboard after a sparkling run on the back nine, reeling off three straight birdies from the 11th and then holing an eagle putt from the fringe at the long 16th.
RORY McIlroy has revealed he requires an MRI scan to determine the extent of a back injury which could rule him out of Europe's biggest event.
But the world number 13 then bogeyed the 17th and 18th to card a second round of 71 and finish five under par alongside Ian Poulter, who eagled the 16th in a superb 67.
World number one Dustin Johnson shot 71, while Rory McIlroy missed a two-foot tap-in at the 10th hole en route to a 73 in his first start as a married man. Garcia also shot 71, thanks in no small measure to his ace at the 17th.
Alex Noren, a four-time victor on the European Tour last season, bogeyed the last for a 72 and the Swede will go into the final round alongside Garcia on five under, while Francesco Molinari (69) and Garcia's compatriot Rafa Cabrera Bello (73) are a further shot adrift.
Poulter is looking to make the most of retaining his PGA Tour card after fellow professional Brian Gay alerted officials to a discrepancy in the points structure used for players competing on major medical extensions.
"I've given him some champagne but he tells me he prefers red wine so he'll get some of that as well", Poulter told Sky Sports.
He told reporters: "I've been struggling with it a bit this week, and I sort of felt it for the first time on Sunday".
After playing just 13 tournaments previous year due to a foot injury, Poulter had 10 events this season to earn 218 FedEx Cup points or United States dollars 347,634 (£269,755) to remain fully exempt.
"Today I was able to free up a little bit and hit some really good shots so hopefully I will be able to do more of the same tomorrow".