The Englishman began the day leading by three but saw his advantage wiped out when he bogeyed the eighth and Nicolas Colsaerts sank his third birdie.
Fitzpatrick, 21, regained the lead with a birdie on the 10th and hit three more from the 13th to finish on 15 under.
Defending champion Alex Noren of Sweden is level with Colsaerts after a 67.
Noren had seven birdies in his five-under round, including four on the trot from the 12th.
He is still well adrift of Fitzpatrick, who parred his first seven holes before dropping just his second shot of the week on the eighth.
The Englishman, who finished seventh at the Masters, bounced back immediately with four birdies in seven holes to move back to the top of the leaderboard.
"I find the front nine more difficult than the back nine, especially in the wind but I stayed patient and got my rewards," he said.
"It's one of the things I've learned since turning pro."
Matt Fitzpatrick extended his lead to five shots at the Nordea Masters in Stockholm by shooting a four-under-par 68 in Saturday's third round.