The 2024 Masters runner-up finished on +2 after his first round, six shots off the lead as many players struggled with the demanding course in Pennsylvania.
Needing a solid round to stay in contention, Aberg bogeyed the second and fifth holes, before finishing the front nine with three successive bogeys.
His back nine was more positive, registering one bogey, holing the rest for par meant he only slipped further down the leaderboard, finishing his round on +6.
A score of +8 for the competition left him tied for 68th, 11 shots behind the leader, Sam Burns, but one shot shy of making the cut for Round 3.
An explanation for Aberg's tough week could be the fact he has been suffering from a migraine, and despite receiving headache tablets from fellow competitor Adam Scott, he continued to suffer out on the course.
The 25-year-old's coach, Hans Larsson, told the Viaplay channel during the round, "It is not the first time (having a migraine), but now it is probably caused by the humid heat that is right now. We hope it subsides, but I see that he is struggling with it."
Aberg's compatriot, Joakim Lagergren, has also missed the cut, following a +9 round of 79 yesterday, which saw him finish on +19 for the tournament, tied for 145th in the 156-strong field.