The pair will play together in Sunday's final group, with Fowler facing an uphill battle after a four-under round of 68.
The American had drawn level with McIlroy during the third round, but the gap remained the same as it was at the start of the day after two closing eagles from the Northern Irishman and a wobble from Fowler.
"I'm definitely satisfied with my game," Fowler is quoted as saying by Sky Sports. "I got off to a great start today through 12 holes. I was playing very solidly and I'm looking to draw on that tomorrow. Being six back is the same position I was in today.
"If I'm able to go out and get off to a good start, maybe I can put a little bit of pressure on him, because he's definitely in control of the golf tournament right now."