Northern Ireland's McIlroy, twice a winner in seven US PGA starts, bogeyed the last for a one-under 69 to finish three over and miss the cut by one.
American Walker also bogeyed the 18th for a 66 and nine-under total, matched by Streb who birdied his last for 63.
Defending champion Jason Day had eight birdies in a 65 to get to seven under.
The Australian world number one is tied third with Argentina's Emiliano Grillo (67), while Open winner Henrik Stenson of Sweden is one shot back after carding a second three-under 67 to move to six under.
Germany's Martin Kaymer (69), who won this tournament in 2010, and Americans Patrick Reed (65) and Brooks Koepka (67) are four adrift on five under.
Wales' Jamie Donaldson (67) is the highest-placed Briton at the final major of the season on four under, one ahead of world number three Jordan Spieth, who also shot 67.
With the cut mark hovering between one and two over par, McIlroy, who holed a 30-foot putt on the 17th to get to two over, thought he needed another birdie on the last.
The four-time major winner hit his second on the par-five 18th into greenside rough and took three more shots to get on the green before holing out for a bogey.
"I thought I needed to make four, so that's what I was trying to do," said the 2012 and 2014 US PGA champion.
"It was a tough lie. I hit the first one as hard as I really could considering how close the pin was to the edge of the green."
The world number four went straight to the practice green after taking 35 putts in round one but he said his efforts on Friday, when he took 30, were "pathetic".
"Putting let me down at [the US Open in June at] Oakmont and then putting let me down here again," he said.
"My tee to green game - there's not much wrong with that. It's pretty solid. If you had given anyone else in this field my tee shots this week, they would have been up near the top of the leaderboard.
"It just shows you how bad I was around the greens."
The Swede was grouped with the year's other two major winners - Masters champion Danny Willett and US Open victor Dustin Johnson - and he outscored them on both days.
He dropped to one under par after three-putt bogeys on the 12th and 13th holes but a three-foot eagle putt on the par-five 18th, his ninth, followed by three birdies on the front nine, moved him one clear of the field.
"I got off to a bit of a wobbly start and stood over a six-foot putt on the 14th to avoid going three over, so I'm quite happy that went in and I turned it on from 18," said the 40-year-old, who won his first major at Royal Troon two weeks ago.
"That could easily have gone the wrong way but I was hanging in there and got the good stuff coming in."
Willett birdied the ninth to card a 70 and make the cut on one over, but pre-tournament favourite Johnson is going home after adding a 72 to his opening 77 for a nine-over total.
Neither American has never won a major and while Walker has five victories on the PGA Tour, Streb has just one and has missed nine cuts in 23 events in 2016.
Walker, 37, made a solid start to round two with two birdies and seven pars in his opening nine holes before moving clear of the field with a run of three successive birdies from the 12th.
He pulled his tee shot on the 17th into a hospitality area and escaped with a free drop and par five but an almost identical shot on the last was not so lucky, ending up in a lake and resulting in a dropped shot.
"The finish wasn't what I was looking for, but it's fine," said Walker. "I think you take 66 at any tournament all day every day. So it's good.
"I will watch the leaderboard on Saturday. I don't think that's a big deal. I enjoy watching it. I think you need to know where you are at."
Streb started on the 10th and had four birdies and a bogey in his opening nine holes and closed with three in four holes to become the 30th player to card a 63 in a major - no player has ever shot a 62.
The 29-year-old, who missed the cut at each of the first three majors of 2016, said he turned up this week "just to see if I could play some good golf and have fun".
He added: "Obviously it's going pretty well, but my expectations are pretty low, which maybe is a good thing."
Day was Friday's other big mover, knocking in seven birdies in eight holes from the eighth to sit two off the lead.
"I kind of gave myself a little bit of a kick up the bum with the double bogey on seven," he said.
"It was a bit of a mess but to come back and birdie eight and nine made things a lot better for me on the back nine."
Former world number one and two-time major winner Spieth had five birdies in his opening nine holes to get to four under par but missed several opportunities to better his score on his back nine, while a bogey saw him close on three under.
"It was a really solid round and I'm back in contention," said the American. "I'm hitting the ball fantastic. I just can't get a putt to go in from beyond 10 feet."
Kaymer, who started at four under, began the front and back nines with bogeys but three birdies in his last four holes lifted him to five under.
"I made a few putts here and there. I enjoyed the last few holes," he said. "It was important for me to finish the way I did."
Andrew Johnston continued to impress in the majors, after finishing tied for eighth at The Open, with a one-under-par 69 to reach halfway at one under.
The Englishman, better known by his nickname 'Beef', started on the 10th and was two under after nine holes. He dropped back to level with bogeys on the fifth and seventh holes, but he then birdied the eighth.
"Every hole, man, I get so many nice comments," said the 27-year-old. "Even after the fifth hole, when I three-putted, they are like, 'Don't worry, Beef, come on, bounce back, you've got this one'. And it's just nice, man. It's a nice atmosphere."
Lee Westwood (70) hit 92% of greens in regulation as he also finished on one under, alongside fellow Englishmen Ross Fisher (73) and Tyrrell Hatton (68).
Andy Sullivan, who reached five under, dropped away with six bogeys in nine holes through the middle of his round before finishing birdie-eagle on the two par-five finishing holes to post a 71 and a two-under total that matched Paul Casey (69).
Scotland's Russell Knox is also playing the weekend after a second 70 left him level par, along with Wales' Bradley Dredge.
English pair Matthew Fitzpatrick (70) and Justin Rose (72) beat the cut by one shot.
Rory McIlroy missed the halfway cut at the US PGA Championship for the first time in his career as Robert Streb and Jimmy Walker lead at Baltusrol.