Day, ranked sixth in the world, completed a seven-under par 65 for a 12-under total of 132 and a one-stroke lead over Hudson Swafford, who held the clubhouse lead when play was halted on Friday on 11-under 133.
Day played his final four holes on Saturday, capping his bogey-free round with a birdie on the par-five 18th.
“We finally got round two in and, knock on wood, that was my first storm delay of the year so hopefully no more would be nice,” Day said. “I came out and played some really nice golf.
“Birdied 15,” he noted of his first hole Saturday morning, “and then obviously birdieing 18 was good. So just happy with where I’m at.”
Swafford, who completed his second-round 66 on Friday, was joined on 133 by fellow Americans Daniel Berger and Chris Stroud. Stroud also posted a 66 while Berger signed for a 67.
Boo Weekley, who was tied for the lead with three to play when the round was suspended, settled for a 70 that left him among a group of eight players sharing fifth place on 10-under 134.
The halfway cut at five-under saw Steve Stricker’s PGA Tour-best consecutive cuts-made streak end at 36. Stricker finished at three-under 141. Other notable names missing the cut included Rickie Fowler, Nick Watney and Jamie Donaldson.
Fowler missed his first cut since last year’s Memorial ending a run of 17 successfully made.
Third-round play got underway soon after the second round ended, with a chance of more wet weather and further delays in the forecast.