The 24-year-old's score is the lowest in relation to par in the history of the US Open, surpassing the eight-under 63 carded by Johnny Miller to win at Oakmont in 1973.
The No. 2-ranked McIlroy and the third-ranked Day also failed to advance to move after struggling for a second straight day.
Casey had tied for the lead earlier in the round with a birdie on his second hole before crashing with a triple-bogey at the par-five 14th.
After the afternoon wave, Casey must have been positively beaming because the long-hitting 39-year-old surprisingly found himself in a four-way tie for the halfway lead at seven-under 137.
Champ, a qualifier from Texas A&M, is leading the 156-player field in average driving distance over the first two rounds at 339 yards, and is tied for eighth on the leaderboard, two shots off the pace at five-under-par after Friday's three-under 69.
He picked up one shot on his first nine, after an opening-round 79, but a double bogey on the fifth and a second-round 75 sunk him to finish 10-over for the tournament.
Shane Lowry proved the best of the Irish and the only one of the starting quartet to make the cut, reaching the half-way stage just inside the cut mark on one over par.
Despite a flurry of late birdies it was not enough to turnaround an erratic round littered with errors and missed opportunities.
But while Casey was relieved after his gutsy fightback, two of the world s top three players - McIlroy and Day - were left contemplating a missed cut. His game showed some rust at Erin Hills, especially off the tee on Thursday, when the last time he hit a fairway was on the 10th hole. I guess it's [rare] you get through a U.S. Open or any major without some kind of hiccup.
A congested leaderboard and the potential for thunderstorms meant an enthralling day was in prospect at Erin Hills as the final groups prepared to go out in round three of the U.S. Open.
First-round leader Rickie Fowler shot a 1-over 73 to fall back to 6-under alongside Jamie Lovemark and JB Holmes, with Hideki Matsuyama a further shot on 5-under adrift after firing an exceptional round of 65. "I think it's going to produce a really great champion".
Triple-bogeys have a way of sinking a round, but somehow that wasn't the situation for Paul Casey on Friday at the U.S. Open. Koepka had the outright lead with four holes left in his round before a bogey on the par-3 sixth hole. Back problems also contributed to an early exit at the Masters when Willett became the first defending champion since Canadian Mike Weir in 2004 to miss the cut.
"I was in the hay too much over the last couple of days", Day told reporters about the knee-high fescue grass lining the fairways at the links-style layout in the Wisconsin countryside.
"If the sun stays like it is and the wind keeps baking this golf course out, it's pretty treacherous on the weekend; which is just what I would like and I think what the rest of the players want to see".
"Shooting a good score today gave me a lot of confidence", Matsuyama said. Schauffele went 26 consecutive holes without a bogey until he rammed his long birdie putt on No. 9 about 12 feet by the hole and narrowly missed the par putt.
"I made two bad swings on the front nine", Koepka said.
McIlroy entered the U.S. Open having not competed since last month's Players. "And unfortunately with where I was hitting it, I wasn't in the way".