McIlroy, who began the day two behind overnight leader Jamie Donaldson, birdied the first two holes and Kaymer, four adrift, eagled the first and fifth.
Both moved alongside Welshman Donaldson, who parred the first four holes, while Lee Westwood was one behind having followed an opening birdie with a bogey on the short third.
Kaymer's putting was deadly. After his 25 footer for eagle on the fifth he saved par from 20 feet at the next, two-putted for birdie on the seventh and holed from over 20 feet again at the eighth.
Six under for his first eight holes, the German was 16 under par and two ahead of McIlroy - second on his own after Donaldson bogeyed the fifth like Westwood, who as a result trailed by four in joint-seventh place.
With mist and rain rolling in - the tee-off times had been brought forward because of the threat of storms - last week's winner Thomas Björn had four birdies in a row from the fifth and cut Kaymer's lead to one.
Westwood came back with birdies at the sixth and seventh and joined McIlroy and South African Jaco Van Zyl in third place, two shots behind.