The 10-shot rule at the tournament means that Mickelson will not make the weekend unless he is in the top 50 on the leaderboard, which he currently is not.
The American shot four-over par on Thursday, and then carded 73 from holes 19-36 to leave him five over for the tournament, level with playing partner Ernie Els.
Out of the Major-winning three ball, Englishman Justin Rose appears to be the only one likely to make the cut after birdies on the final two holes saw him shoot 70 to close on two-over par.
Mickelson parred each of his opening seven holes on his second time around the course, and although he picked up a shot at the par-five eighth, he bogeyed the next hole after finding the trees.
He found a bunker off the tee at the difficult par-three 12th, and then chipped from sand to sand across the green twice on his way to making a triple bogey, his second of the tournament.
Mickelson birdied three out of four holes, but there was a bogey in there at the 16th as well, and he failed to make up any strokes in the final two holes to leave his tournament future in serious jeopardy.
The 43-year-old won the green jacket in 2004, 2006 and 2010.