At the close England were 341 for five on a day when Australian leg-spin great Shane Warne became the first bowler to take 600 Test wickets.
Ian Bell was 59 not out, his Test-best against Australia, after nightwatchman Matthew Hoggard was bowled by a 91mph Lee yorker for four off the last ball of the day.
Andrew Flintoff, England’s man-of-the-match in their two-run series levelling win at Edgbaston, was due to bat next on his Lancashire home ground.
Lee, who had dismissed Kevin Pietersen with the second delivery of the new ball, led the attack with three for 58 after Vaughan won the toss.
Vaughan, who had managed a mere 32 runs in four innings in the first two Tests of this series, faced 216 balls with one six and 21 fours, one all-run, before he holed out to Glenn McGrath at long-on off occasional left-arm wrist-spinner Simon Katich.
It was the 30-year-old’s 15th Test hundred, his sixth as England captain, and fourth against Australia, after three centuries during the 2002-03 Ashes series.
England, looking to build on last week’s dramatic two-run win at Edgbaston which levelled the five-Test series at 1-1, were helped on their way by the unusual sight of Australia dropping several catches, with Vaughan missed on 41 and 141.
Warne made history in his fifth over when Marcus Trescothick, trying to sweep, was caught by wicket-keeper Adam Gilchrist for 63 to leave England on 163 for two.
Gilchrist, who dropped Vaughan, had earlier failed to hold onto a chance offered by Trescothick, on 13, both of those misses off returning fast bowler McGrath.
McGrath also suffered the frustration of bowling Vaughan off a no-ball and later dropping a caught and bowled chance offered by Bell on 18.
Vaughan’s first escape came when Gilchrist, diving to his right, failed to hold an edged cut with England 110 for one in the 29th over.
And next ball, Vaughan had his off-stump knocked over by McGrath only for umpire Steve Bucknor to signal no-ball.
McGrath’s mood was not improved after tea when, having deceived Bell (18) with a split-finger slower ball, he failed to hold the one-handed looping return catch with England 211 for two in the 59th over.
Vaughan played some majestic strokes, including a pulled six off Jason Gillespie. But nine short of his 150 he saw first-slip Matthew Hayden grass a sharp chance from a backfoot forcing stroke off Warne.
Gillespie’s 15 overs cost an expensive 89 runs and the usually miserly McGrath conceded 76 off his 19.
Vaughan added 127 with Bell before his exit left England 290 for three.
Bell, whose previous best against Australia was 21, cover-drove Warne for a textbook boundary before Lee had Pietersen (21) pulling to substitute Brad Hodge.