Woods, who had been sidelined since March after having surgery to repair a pinched nerve in his back, struggled with his driving and short game on a tough Congressional Country Club layout on the way to a four-over-par 75 in the second round.
That left the former world number one at seven-over 149, and well outside the projected cutline of three over.
Woods, whose charity foundation is benefited by the PGA Tour event, had opted to return to the U.S. circuit this week to give himself competitive preparation for next month's British Open, the third major of the year.
"I am really encouraged by what happened this week," an upbeat Woods told reporters after a round that included just three birdies, five bogeys and a double.
"I missed the cut by four shots, that's a lot, but what I was able to do physically and the speed I had and the distance I was hitting the golf ball again, I hadn't done that in a very long time.
"I needed to get back into competitive feel ... to hit shots and shake some stuff off and see how things were. I've had no setbacks. I got my feel for playing tournament golf."
Woods headed into Friday's second round facing an uphill battle to make the cut after opening with a 74 and he lost further ground when he double-bogeyed the fifth before dropping another shot at the eighth.
He briefly raised hopes of conjuring a stirring fightback as he drained a 26-foot birdie putt at the ninth, then followed with a 12-footer at the par-three 10th.
However Woods continued to miss fairways off the tee and, with the lush rough at Congressional posing all sorts of problems for recovery shots, he went on to bogey the 11th, 12th, 13th and 14th.
Though he birdied the par-five 16th after reaching the green in two and two-putting, he lipped out a birdie attempt from just four feet at the 17th before parring the last.
"I made a ton of simple little mistakes, misjudging things and missing the ball on the wrong sides, not being able to get up and down on simple shots," said the 14-times major winner.
"The thing I was worried about the most was hitting driver, and I roasted it, the last two days I hit it really well. The short game was off.
"As I said, I made so many little mistakes this week, but that is something I can rectify, and get that fixed for the British (Open)."
Woods has been increasingly plagued by injuries in recent seasons as the wear and tear of years on the tour have begun to take a toll.
He failed to finish the PGA Tour's Honda Classic at Palm Beach Gardens in early March, quitting after 13 holes in his final round, then tweaked his back again on the last day of the WGC-Cadillac Championship in Miami just one week later.
Woods pulled out of the March 20-23 Arnold Palmer Invitational, a key lead-up tournament he has won eight times, in the hope that he could play at the Masters before he opted to undergo surgery on March 31.
He ended up missing the Masters, in April, and the U.S. Open at Pinehurst earlier this month but will compete in the year's third major, the British Open at Hoylake, from July 17-20.
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