The German birdied the last to card a three-over 74 that left him at even par, with Padraig Harrington, Vijay Singh, Steven Alker and Phillip Archer his nearest challengers.
Harrington, who is bidding to become just the fifth player to win both The Open and Senior Open, was one of seven players to manage a level-par round of 71 on the Welsh coastline.
It was the first time no player has produced an under-par round in the Senior Open since the first round in 2005, when Tom Watson went on to win at Royal Aberdeen.
“It was a tough day for everybody,” said Cejka, who is targeting his third Senior Major Championship title to go along with his wins at the Regions Tradition and KitchenAid Senior PGA Championship in 2021.
“Still on top of the leaderboard, so I’m pleased.”
Cejka carded four birdies and seven bogeys, having begun the day one shot adrift of second round leader Alker.
He added: “I think for everybody, winning a major is special. Winning a couple years ago, it was great. In Europe, I’d like to win and it would be special.”
Harrington made eagles on the sixth and 18th and chipped in for a birdie on 14 in an eventful round as he looks to emulate Bob Charles, Gary Player, Watson and Darren Clarke as the fifth player to lift both the Claret Jug and Senior Open trophy.
Playing his third event in as many weeks, the Irishman cited mental fatigue for some uncharacteristic mistakes and knows he will have to be at his best with further inclement weather forecasted on Sunday.
“I’m going to try and recover now again, between now and tomorrow,” he said. “Come out fresh. It’s not a given, but I’m hoping that I’ll be sharp, real sharp.
“I didn’t realise until I got the bad news that it’s actually going to be worse tomorrow. I’m not sure if that’s true. But if it is, you’ve just got to be really sharp mentally.”
Singh held a three-shot lead at one stage after he reached four under as he followed a birdie at the sixth with a hole-out eagle at the seventh.
But the Fijian then dropped four shots in a five-hole stretch from the 13th, before closing with a birdie to join the group at one over.
“We don’t normally play wind like this, especially me, I haven’t played in conditions like this for a long, long time,” he said. “But you have to control your ball. It wasn’t easy. Putting was really difficult.”
Despite the field facing gusts up towards 30mph, there were still moments of brilliance as second-round leader Alker made a hole in one at the 15th, the 14th ace in Senior Open history.
However, the Kiwi struggled to a 76 which included a bogey-bogey-double bogey start but his ace and a closing birdie maintained his hopes of a second Senior Major win.
Archer, who is targeting victory on his first appearance at Europe’s only Senior Major Championship, mixed four birdies with two bogeys and a double bogey in his 71.
“I enjoyed it to be honest,” he said. “Took on the challenge a little bit. I have got my best mate and my coach on the bag and we embraced it.”
Jerry Kelly, a two-time Senior Major winner, and Senior Open debutant Greig Hutcheon are two shots off the lead after they recorded a 71 and 75 respectively.
Paul Lawrie is in a three-strong group one shot further back, while Bernhard Langer is alongside a bunch of players at four over as he looks to win the Senior Open at Royal Porthcawl for the third time.
Emanuele Canonica made an albatross when he holed his second shot on the par five 15th but the Italian dropped six shots in his next four holes to finish at six over.
