While McIlroy admitted to feeling the pressure of trying to satisfy another expectant gallery, playing-partner Howell thrived on the atmosphere to card a sparkling 7-under 64.
That took former Ryder Cup player Howell to 11-under-par 202 and into a share of a two-shot lead with Australian Richard Green and fellow Briton Simon Dyson who both carded 67s.
McIlroy, by contrast, stumbled to a 72 with two double-bogeys on his card and the weekend's top attraction at Killarney trails the leader by eight strokes going into Sunday's final round.
"I don't mind saying it was a superb round," a delighted Howell told reporters after plundering seven birdies.
"Especially playing with Rory. He's got an intimidating game when he's on.
"But I really enjoyed being in the thick of it, I think I did get inspiration from the atmosphere out there. There's expectation on Rory at home, though. It's difficult, I'm sure."
McIlroy conceded he had struggled to satisfy the fans who had again turned out in huge numbers to cheer on the 22-year-old.
"You want to do so well for them and they want you to do so well," he said, adding: "I felt at times I was almost trying a little too hard."
It was a change of roles for the two players from what happened at the Congressional in June.
"I did qualify for the US Open, but while Rory was doing miraculous things I was absolutely shocking," Howell said.
It has been a rough ride for Howell, a member of Europe's winning 2004 and 2006 Ryder Cup sides against the US, with various injuries affecting the 36-year-old Englishman.
After claiming his fourth European Tour title in 2006 his place in the world order spiralled so far downwards he has become better known for television punditry and after-dinner speaking.
Howell, though, fifth in the Qatar Masters earlier in the season, hopes he is on the way back up the world rankings on which he once held ninth place.
The top trio holds a two-shot advantage over Britain's Stephen Gallacher. Defending champion Ross Fisher of Britain is three behind with Dane Soren Hansen and overnight leader Marcel Siem of Germany. Siem double-bogeyed the last after a wild approach.
Killarney's other big crowd-puller, 2010 US Open champion Graeme McDowell also disappointed the home gallery with a 72 to be eight off the pace.
In White Sulphur Springs, West Virginia, Brendon de Jonge shot a 3-under 67 and Webb Simpson had a 68 to share the lead at 7 under midway through the Greenbrier Classic.
Among those failing to advance to weekend play were Phil Mickelson, whose streak of making 17 straight cuts ended, and defending champion Stuart Appleby. Both finished 3 over, missing the cut by two strokes.
De Jonge has played the Old White TPC course many times and he finished third in last year’s inaugural tournament at 17 under. It was one of three third-place finishes in 2010 that helped him earn a career-best $2.2 million.
Simpson made three birdies on the back nine.
First-round leader Trevor Immelman made just two birdies, shot 70 and was at 6 under.
Tied at 5 under were Scott Stallings (65), Michael Letzig (66), Gary Woodland (70), Brian Davis (64) and Derek Lamely (70).
