England were restricted to 255 by a hostile bowling spell from Mitchell Johnson, but the Australians made heavy weather of their reply on a slow MCG pitch.
Veteran opener Chris Rogers crawled to his third half-century of the series following the cheap dismissals of David Warner (9), Shane Watson (10) and skipper Michael Clarke (10).
Nearing tea, Rogers scampered through for a single off spinner Monty Panesar to claim his 50 off 133 balls.
At the interval, Australia trailed England by 159 runs at 96 for three with Rogers unbeaten on 50 and Steve Smith not out 14.
England knuckled down to keep the Australian batsmen on the leash after their last four wickets fell in the opening half-hour of Friday's play.
Jimmy Anderson surprised Clarke with a delivery that shaped in and collected the top of off-stump in the 26th over of the innings.
The Australia skipper was pinned down by disciplined English bowling with his 10 runs coming off 34 balls.
England, resuming at 226 for six, meekly succumbed to be all out for 255 with Johnson taking five for 63 in a withering four-over morning spell of three for four with two maidens.
Among the England wreckage was the wicket of Pietersen, out bowled going for a wild slog for 71 after adding just four runs to his overnight score.
In the 13 overs to lunch, Australia lost the wickets of Warner and Watson.
Warner top-edged Anderson high into the air to give recalled wicketkeeper Jonny Bairstow a straight forward catch.
Bairstow took his second catch dismissing Watson off the bowling of Ben Stokes.
Johnson now has taken 28 wickets at 14.96 for the series.
He had a double-wicket breakthrough in his opening over of the day, removing Bresnan (1) and Pietersen (71).
Bresnan received a brutish rearing delivery first-up and he fended it away in an act of self-preservation to George Bailey at short leg.
Pietersen, who batted cautiously on the opening day for his 67 off 152 balls, added a streaky boundary off Ryan Harris before he fell to Johnson, four balls after Bresnan's dismissal.
Pietersen went for a lusty swing and Johnson knocked back his middle stump as England's hopes slumped with the big loss of their showman batsman.
Pietersen, who passed Geoff Boycott as the fourth all-time England run-getter on the opening day, batted for 254 minutes before throwing away his wicket.
Johnson then trapped Stuart Broad leg before wicket for 11.
Panesar, who took an eye-watering blow in the groin from paceman Peter Siddle, was the last wicket to fall.
Panesar shouldered arms to spinner Nathan Lyon and was bowled for two leaving Jimmy Anderson 11 not out.