Beljan, fighting for a place on the tour for 2013, suffered an elevated heart-rate and shortness of breath, prompting him to lay or sit down between shots on the way to a three-shot lead at 12-under 132.
"A couple of times when he was putting, I thought he might just pass out," his caddie Rick Adcox said. "On 16, he put the ball down to putt, marked it and walked away. I thought maybe he was going to get sick there."
It was unclear whether the 28-year-old American, who leads seven players tied on 135, would return to play the weekend.
Beljan complained of breathing difficulties before his round and called for a paramedic halfway through but battled on to claim top spot on the leaderboard.
Late last year, Beljan said he had suffered a bout of Valley fever, a fungal infection that can cause shortness of breath, rash and joint aches.
"I've got to give Charlie credit for what he did," Adcox said. "I thought he was going to quit out there a few times. He sat down on the bag a few times. He laid down a few times."
Beljan, who won the 2002 US Junior Amateur title, was 139th on the money list entering the event, with only the top 125 assured of keeping their full cards for next year.
Beljan needs to finish somewhere inside the top 10 at Lake Buena Vista to secure his card, according to current projections.
Three shots back on nine-under were Americans Charles Howell III (67), Harris English (67) and Mark Anderson (67), along with Japan's Ryuji Imada (66), Swede Henrik Stenson (67), South Korea's Charlie Wi (71) and Australian Matt Jones (64).
Anderson, Imada and Jones all entered the week outside the top 125 and need to remain high on the leaderboard to have a chance at reclaiming a tour card.
"I finally made some putts. First time this year, it feels like," said Jones, who matched Beljan's 64. "It was a good time to do it. Better late than never, so hopefully we can keep going."
Several players at the fringe of the money list will have nervous weekends after missing the cut.
Americans James Driscoll (120th) and Billy Mayfair (125th), along with Australia's Rod Pampling (124th), have left their fates in the hands of others.
Two-time heart transplant recipient Erik Compton of the United States missed his last chance to automatically qualify by adding a 76 to his opening 71 to miss the cut which was set at one-under 143.
Imada, a US PGA Tour winner four years ago, said one good weekend could mean a lot.
"It can turn your whole year around. I'm in position to do that, but still got a long ways to go."