World number one Woods and second-ranked McIlroy each carded a level-par 70 on a brutally challenging Merion Golf Club layout where finding rough was a virtual guarantee of a bogey with tough pin positions to tackle on the greens.
Both players were happy with their respective positions going into the final two rounds of the year's second Major, despite finishing at three over par - six strokes off the early lead.
"I played well,' Woods said after mixing three birdies with three bogeys on a sun-drenched, breezy afternoon at Merion that followed a week with rain.
"I just made a couple of mistakes out there today, but I really played well. Maybe I could have gotten one or two more out of it, but it was a pretty good day.
"They've really tried to protect the golf course, with it being as soft as it is. And they've given us some really, really tough pins."
Asked if he liked his chances heading into the weekend as he continues his bid for a 15th Major title, but his first in five years, Woods simply replied: "Yes."
Though Merion is hosting the US Open for the first time in 32 years after long being viewed as too short to stage a Major, Woods disagreed with suggestions that the iconic East Course would be exposed by the power hitters in the modern game.
"Unless you have played practice rounds out here and you've seen the golf course, you don't realise how difficult it is," the three-times US Open champion said.
"The short holes are short, but if you miss the fairway, you can't get the ball on the green. And the longer holes are brutal.
"And this is probably the stiffest set of par-threes that we ever face. And then they've thrown some of the pin locations in that they have and it's really tough."
McIlroy, the 2011 US Open champion at Congressional, felt the combination of tricky pin positions and swirling breezes had been the biggest factor in pushing up the scores in the second round.
"They put the pins in places that even when you hit it close, you had a tough putt for your birdie or your par or whatever," the 24-year-old said after offsetting four birdies with four bogeys.
"The wind is up, and it's tough to gauge this wind. It swirls a little bit in these big trees and it's hard to pull a club sometimes. That's why I think you're seeing the scores rise a little bit today.
"And if you don't hit the fairways here, you're not going to score. If you do hit the fairways, it's still a big challenge from there."
Like his good friend Woods, McIlroy was also delighted with his two-round total on a challenging venue where the average score in the second round was almost five over par.
"I'm very happy," said McIlroy, who clinched his second Major title at last year's US PGA Championship to put the seal on a stellar 2012 campaign which he ended by leading the money lists on both sides of the Atlantic.
"Right in there for the weekend. I don't think I'll be too far away by the end of the day. I'm in a nice position going into the last two days."
McIlroy and Woods attracted huge galleries at Merion after being grouped with Masters champion Adam Scott for the first two rounds in a mouth-watering combination of the world's top three players.
However, Australian Scott has not fared as well, struggling to a 75 to finish at seven-over 147.
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