The American appeared set for a big week after matching the five-under 67 of playing partner Rory McIlroy in the opening round, and he was going along nicely on day two until his challenge was derailed at the eighth.
Fowler pulled his drive into the shrubbery and was unable to find his first ball as he ran up a costly triple-bogey eight, and he made the cut with nothing to spare after dropping two further shots on the inward half.
The 26-year-old continued to struggle in the third round, carding two bogeys and a double-bogey at the 10th, although he lifted his spirits with a closing eagle to salvage a one-over 73.
“It’s just golf, it was a little rough today,” said Fowler, who will go into the final round in a tie for 67th on one under par.
“The course is great, nothing has changed. I just got into a bad rhythm for a couple of days. I made some good swings on the last.”
Fowler will head back to the United States following Sunday???s final round to begin his preparation for the Masters in April, and he already has his sights set on making the Presidents Cup team in October.
When asked about his top targets for 2015, he added: “I definitely want to win, play well through to the FedExCup and make the President’s Cup team.”
Fowler finished in the top five in all four majors last year, but he is without a win since claiming his maiden PGA Tour title when he edged out close friend McIlroy at the Wells Fargo Championship in 2012.
He has hinted at playing more regularly on the European Tour, but he is confirmed only for the Irish Open in May this year while he is also expected to play in the Aberdeen Asset Management Scottish Open in July.