Lowry, 22, is a plus-five handicapper but he looked every inch the professional as he outshone a host of big names including compatriot Padraig Harrington and American John Daly with a superb 10 under par 62 in the second round.
While Harrington and Daly missed the cut, Lowry was in the form of his life at the Baltray links and matched the lowest round ever achieved by an amateur on the circuit, by German Sven Struver 20 years ago.
"It's like a dream really - when do I wake up?" Lowry said after taking a two-stroke lead over England's Robert Rock and Welshman Jamie Donaldson.
"This is as good as I can ask for and it's hard not to think about winning now, but I'm just going to go out and play as best I can."
Listed at 16th in the world amateur rankings, Lowry's 36-hole total of 129, 15 under, is the best by an amateur in Tour history.
It would also have broken the course record but for the fact that just over an hour earlier Northern Ireland's Graeme McDowell blitzed an incredible 61 - the lowest round of his professional career and an unbelievable 16-stroke improvement on his opening 77.
Those were not the only two dramatic rounds, however.
Former Open champion Paul Lawrie won himself a 40 000-pound car for a hole-in-one on the 17th as he kept alive his hopes of a first victory for seven years.
Lawrie had his second successive 66, but that was three behind Lowry's 15 under par aggregate.
Earlier, Italy's Francesco Molinari, the first round leader, was disqualified for signing for a wrong score.
Molinari double-bogeyed the 13th hole but did not notice that the six had been put down for his score at the 12th instead.