The leading duo were hotly pursued by Jason Day, who finished two shots behind the pair before the hooter sounded and play was suspended for the day due to the fading light. Both men opened with 70 on Thursday.
Kevin Kisner, who shared the first round lead with Thorbjorn Olesen with 67 each, pulled ahead on Friday morning as scoring continued to be tough at Quail Hollow, a regular venue on PGA Tour, but hosting a Major for the first time.
With 25 players unable to complete their second round because of the delay, Day is likely to start his third round in the second-last group out, trailing joint leaders Hideki Matsuyama and Kevin Kisner by just two strokes.
Down the stretch he pulled off four birdies to launch him back into contention.
The 29-year-old Australian hit his second shot into a shrub and had to take a penalty drop en route to a crippling quadruple-bogey eight. If he can find this zone this weekend, where bad tee shots still find the middle of the fairway, and bad irons are still in birdie range, there isn't anyone in the world who can stop him.
However, last week's WGC Invitational victor Hideki Matsuyama was threatening to challenge Kisner's supremacy before a weather delay halted him in his tracks.
Kisner hasn't fared well in a dozen major appearances, but that hasn't changed his attitude when it comes to vying for the biggest wins in the sport.
Asked how he ended up playing with McIlroy in practice, 2016 Challenge Tour victor Smith added: "A good friend of mine knows Rory's caddie (Harry Diamond) so I got his contact details and chatted to him and managed to hook it up".
"I kind of accept the fact that I'm essentially out of this tournament pending some form of insane stuff the next couple of days", he said. I ended up leaving a lot of putts short. "I think players spend too much work into figuring out golf courses, instead of just getting the ball in the hole". "Hopefully he slows down a little bit and gives the rest of us a chance, but I still feel I'm there".
Kisner, meanwhile, used his "Texas wedge" from off the green to sink a 47-foot putt at the par-five seventh - his 16th hole - and vault clear of the field, at least for a while.
The Japanese rescued par at the ninth hole with a 22-foot putt, then began his birdie charge with a 12-foot putt at the par-four 12th and six-footers at the par-three 13th and par-four 14th before a storm halted play.
Kisner sank a five-footer for birdie at the par-5 15th then parred the next nine holes before his dramatic eagle at seven.
Kisner, 33, endured four runner-up finishes in 2015 before a breakthrough first US PGA Tour victory at Sea Island, Georgia, in his 109th attempt. 14-16, only to be stuck with a double-bogey on the final hole.
"Kis is on fire right now", said McIlroy. "It's a tough track where they are putting these flag sticks".
USA star Rickie Fowler fired a 70 to stand on 139, five off the pace.
Louis Oosthuizen joined Thomas at 5 under with an even-par 71.