Day's charge at Conway Farms had been halted by a storm on the first day of play on Thursday, with the Australian finishing on a 10-under-par 61.
The USPGA Championship winner shot four birdies and an eagle on the back nine, and teed off on his final first-round hole - the ninth - before the horn sounded.
He resumed play on Friday needing to chip for an eagle to take him to 59 but, playing from wet rough, saw his attempt fall short.
Day then missed an eight-foot putt for birdie, leaving him to settle for 61 and a four-shot lead over Daniel Berger and Jordan Spieth.
Having also triumphed at The Barclays last month, Day could move to world number one should he preserve his lead and claim victory at the FedEx Cup event.