Chapchai was one of 78 players, including world No 1 McIlroy, stranded on the course on a storm-threatened opening day but he returned to complete a bogey-free six-under 65 for a one-shot lead.
Resuming on three-under after five holes, the stocky 29-year-old added three birdies, including one at the par-five 18th, to move a stroke clear of overnight leader Thomas Bjorn of Denmark before rushing off to start his second round.
Briton Simon Khan, Spaniard Pablo Martin and Thailand's Chinnarat Phadungsil, who all completed their opening rounds yesterday before the weather halted play, sit a further shot back in a tie for third place.
McIlroy was even par when he resumed on the ninth hole and the Northern Irishman was steady for the remainder of his round, birdying the par-four 11th and parring the other holes to register a one-under 70 and join a big group tied for 21st.
Chapchai often struggled to contain his temper when things were going wrong on the course but the practicing Buddhist explained that regular meditation had helped soothe his nerves.
"Yes, I've been going (to the monastery) a lot to calm myself out," Chapchai said. "I used to be very hot-tempered. My parents sent me to the monastery and I became a monk for a while. My temper is better now."
He did not fare as well in his second round with two birdies and two bogeys at the turn. Simon Dyson reeled off four unanswered birdies in his first 13 holes to join Nirat on six-under-par, before the thunderstorms rolled in again to bring a further halt to proceedings.
Before he started his second round, McIlroy admitted the break in play had not affected his concentration but he was a little disappointed with his green play.
"With the weather we have here at this time of the year, you have to expect some disruptions," he said. "I actually played pretty well from tee to green, just didn't really hole any putts, which was a bit frustrating."
Back onto the Sentosa course as the tournament tried to make up for lost time, the 23-year-old hit trouble on the back nine.
After a bogey on the 12th, he double-bogeyed the 458-yard next and at two-over was outside the projected halfway cut mark.
McIlroy hit a birdie at the long 18th, however, and hit his approach to the 429-yard first to within three feet of the flag.
He missed the chance to make it a hat-trick of birdies on the short second, but with more lightning in the area the suspension came as he played the next and interrupted the event even earlier than it did yesterday.
Play resumed at 3.30 local time after a delay of nearly two hours, but it was only for 15 minutes as another storm cell arrived.
McIlroy had time to birdie the 480-yard third, hitting another superb iron to three feet and moving to one-under, but his final shot before the second suspension was a drive down the long fourth that was pulled left towards the hazard.
Shane Lowry, having played 12 holes in his second round, was one over for the day to go with his opening one-over 72. Pádraig Harrington, outside the projected cut on three over, had yet to start his second round.