With England chasing an improbable target of 504 to avoid defeat in the third Test in Perth, Pietersen put on a brisk 45 before holing out to Ryan Harris on the long-on boundary off the bowling of Nathan Lyon.
England finished the fourth day on 251-5, leaving Australia just five wickets short of an unassailable 3-0 series lead, and Boycott once again pointed the finger at Pietersen.
"You could see it coming with Kevin Pietersen," the 73-year-old Yorkshireman, a regular critic of the South Africa-born batsman, told BBC radio.
"Brad Haddin turned to (Michael) Clarke to say something, and they brought long-on up to mid-on. Pietersen took the bait and got away with it; a mishit for three. His brain was scrambled.
"He won't play in a careful, controlled manner. It's as selfish as you can get. You wonder what (head coach) Andy Flower and (batting coach) Graham Gooch are saying to him. Are they strong enough to say something to him?"
Pietersen, 33, has performed fitfully in Australia, with a second-innings 53 in the second Test in Adelaide his highest score in the series to date.