It left the former Ryder Cup captain from Northern Ireland on six over par overall, with the cut at two under par.
Starting on the 10th, Clarke began his second round steadily but then had a double bogey on the par-four 16th and dropped another shot at 17.
Martin Kaymer of Germany leads the tournament on 12 under par.
Rafa Cabrera Bello of Spain is on 11 under par, with Paul Dunne of Ireland one of three players a shot further back.
Wicklow man Dunne picked up four shots on his first nine, including an eagle on the 18th hole.
He finished with a six-under-par 66 to lie on 10 under along with England's Tommy Fleetwood and Kiradech Aphibarnrat of Thailand.
Darren Clarke has missed the cut at the Abu Dhabi Championship after a second successive round of 75.