Mickelson took over the leaderboard with a birdie on the long par-3 17th at Merion Golf Club, then parred the final hole as his closest competitors stumbled down the stretch.
The five-time U.S. Open runner-up finished 54 holes of the year's second major at 1-under-par 209.
Luke Donald also had trouble in the late going Saturday, dropping three shots over the final two holes to finish with a 71. He shared fifth place at 1-over 211 with Justin Rose (71) and second-round co-leader Billy Horschel (72).
Tiger Woods, seeking his fourth U.S. Open title, fell to a 6-over 76 and ended in a tie for 31st place at 9-over 219.
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