Simon Jones was introduced opposite Flintoff and dismissed Damien Martyn with his first delivery, caught by wicketkeeper Geraint Jones for just 2.
Simon Jones then snared the wicket of Michael Clarke leg before wicket for 11.
Australia reached 97-5 by lunch but then lost the wickets of Gilchrist, Warne and Simon Katich.
Lee was dropped by Pietersen at slip off the bowling of Harmison but, on the next ball, Harmison had Lee caught behind for 3.
Australia's selectors kept faith in Gillespie, who lined up for his 19th straight test after struggling for form early in the tour and suffering an injury scare when knee soreness forced him to miss training on Tuesday.
He made just 1 before he was trapped lbw by Harmison, leaving McGrath on 10 not out.
"The team is pretty disappointed the way the second half of the game went but there's nothing we can do about it now," Harmison said.
"Hopefully tomorrow we come out and try and get as many runs as we can and put Australia under some more pressure again."
The tally of 17 wickets was the highest number to fall on opening day of a Lord's test since England played India in 1936.
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