As overnight leaders blew up on the PGA Centennary Course, Cejka flourished, shooting the low round of the day, a 6-under 66.
At 12-under-par 204, he enters Sunday one shot better than Paul Casey (67) and two better than Justin Rose (68), while five others are three back at 9-under.
My season started pretty poorly but from the Open on I have felt much more confident, said Cejka, whose best finish of the season was a 13th-place showing at the 130th Open Championship.
At Lytham I was playing with the big boys, the superstars of golf, and I almost beat them. Of course that gave me a big boost and we will see how far I can take it tomorrow.
Cejkas good play began immediately at Gleneagles, with birdies over his first two holes of the day. He added another pair of red numbers at the 8th and 9th to go out in 32.
Three more birdies on the back nine ' including one at the closing par-5 18th ' offset his only mistake of the day, a bogey at No. 13, and saw him end with 66.
I think the difference is that I have been putting well,' said Cejka. 'In fact Ive been putting well the last few weeks after the Open. It is so far so good and Im really happy to be in this position but well just have to see what happens tomorrow.
The entire complexion of the leaderboard changed on Day 3, as the top three players did nothing to help their chances of victory.
Gary Evans, who began the day with a one-shot lead at 11-under, shot 77 Saturday to finish in a tie for 16th at 5-under.
Peter Fowler was even worse. The Australian began at 10-under, but ended at 4-under thanks to a fat 78. Finally, Mark Mouland, who started the day at 9-under, was not quite as bad, but a 73 will have him entering Sunday four shots off the leading pace.
One other who was not particularly fond of his third round was Scotlands Andrew Oldcorn.
At 14th on the European Ryder Cup points list, the veteran entered the day in good position just four shots back. However, like the others, he too shot a 1-over 73 Saturday to fall to 6-under, and will now need a spectacular round on Sunday to gain the kind of points that he needs to make the team.
At No. 26 on the list, Rose might now be the most significant contender entering the final day.
However, nothing short of a win and a strong showing at next weeks BMW International Open will suffice for the young Englishmans hopes of being selected by captain Sam Torrance.
Full-field scores from the Gleneagles Scottish PGA Open