The Northern Irishman, winner in his last three starts including The Open and US PGA Championship, shot a three-over-par 74 and trailed Van Pelt by nine strokes.
Among the long queue tied for second at five-under 66 in the opening tournament of the four-event FedExCup play-offs were Jim Furyk, who stood third on the points list, his old Ryder Cup team-mate Hunter Mahan and England's Paul Casey.
They were joined by Brendon de Jonge of Zimbabwe and Americans Charles Howell III, Cameron Tringale, Ben Martin and Brendon Todd on a course softened by overnight rain.
The 25-year-old McIlroy blamed his poor play on a lack of preparation and not on fatigue despite taking time to celebrate his blistering run and attending to added business commitments.
"I think it's more to do with just not putting the adequate time into my game over the past week for obvious reasons," he said after his first over-par round in competition since the final round of the US Open in June.
"So I'm going to grab a bite to eat here and go to the range this afternoon and work on a few things and really catch up on some practice that I probably missed out on over the past week.
"I probably just needed to give myself a little bit more time," added McIlroy, who did some promotional work with Tiger Woods and also appeared on a late night talk show with him.
"But I wasn't going to do that. I was enjoying myself."
Van Pelt, refreshed after two weeks off and a successful fishing trip on the murky East River, said touring the classic A.W. Tillinghast Ridgewood Country Club course took him back to his youth.
"The course I grew up on is similar," the Indiana native said. "A lot of trees and bent grass.
"I love coming up here to bent grass ... and stuff that I'm used to. Kind of takes me back to being a kid."
Entering the elite 122-man field in 104th place, Van Pelt said he had no expectations, content to be included after a dismal start to a season marked by five missed cuts in a row.
"As poorly as I played at the start of the year, I'm just kind of glad to be here," he said, illustrating his relaxed approach by taking up an invitation to go fishing.
"I went striper fishing on Tuesday. I caught some fish in the East River, so maybe that was my good luck charm this week."
Mahan used a string of three birdies from the 15th to grab a share of the lead, relying on a steady driver to stay out of the thick rough.
"Hit fairways, hitting greens, giving yourself a lot of good looks is the best way to play this golf course," said Mahan, who said he benefitted from perfect greens, being in the third group off the tee.
Tringale, playing in the same group as Mahan, birdied the last two holes for his 66. "We had great rhythm in the round. Everyone was playing well and hitting a lot of quality shots, so it kind of felt like I was just trying to keep up."
- Sports & Recreation
- Hunter Mahan
- Cameron Tringale
- Brendon Todd