Root and Pietersen both played terrible shots in the circumstances off Nathan Lyon and Peter Siddle respectively to be out for 15 and four to now leave England at 4-116 at lunch on Day 3.
Opening batsman Michael Carberry was looking good at the crease but became England's fourth wicket to fall just before the interval when he was out for 60 thanks to a scintillating catch from David Warner.
That leaves England now in desperate trouble at 4-116 in reply to Australia's 9(dec)-570.
England is still 454 behind Australia's first innings score and still requires a further 254 runs to avoid the follow-on.
Now at the break, Ian Bell remains not out on 29 and debutant Ben Stokes is with him and yet to score.
After Australia piled on 570 in its first innings before declaring with just over 20 overs remaining on Day 2, England lost captain Alastair Cook before stumps with a beauty of a delivery from Mitchell Johnson.
That meant England came into the third day on 1-35 with plenty of hard work, patience and restraint were required to hang in there, and make Australia have to work hard for their wickets.
However, that message didn’t appear to get passed down to new No. 3 batsman Root.
Shortly after Australian off-spinner Lyon was brought on to bowl, Root attempted a slog sweep shot looking for easy runs and he only managed to hit it up in the air for Chris Rogers to take a comfortable catch in the deep.
Root had been bogged down somewhat facing 80 deliveries for his 15 with just the one boundary, but his was a terribly applied shot in a time when restraint was required from the English batsman.
The visitors were then 2-57 and shortly after 3-66 when Pietersen played an even worse shot to be out for four.
He had already survived a close caught behind appeal that was struck down, but shortly after he sauntered down the pitch and tried to clip Siddle in the air through mid-wicket. He only managed to hit it straight to George Bailey, though, who took a juggling catch.
Bell came to the crease then for England and immediately took the attack to Australia and hit Lyon out of the attack and was scoring at better than a run a ball for some time, but he soon lost his partner at the other end.
Carberry was looking good particularly when playing strokes through the off-side field and he then made good connection on a pull shot off Shane Watson just before lunch, but Warner pulled off a spectacular one-handed catch to dismiss him for a well-made 60.
AUSTRALIA FIRST INNINGS 9(dec)-570
ENGLAND FIRST INNINGS
A COOK b Johnson 3 (11)
M CARBERRY c Warner b Watson 60 (144)
J ROOT c Rogers b Lyon 15 (80)
K PIETERSEN c Bailey b Siddle 4 (12)
I BELL not out 29 (38)
B STOKES not out 0 (6)
Sundries (1lb 1w 3nb) 5
Four wickets for 116
Fall: 9 (Cook), 57 (Root), 66 (Pietersen), 111 (Carberry).
Bowling: M Johnson 12-6-24-1 (1w 2nb), R Harris 11-7-12-0, N Lyon 13-3-49-1, P Siddle 9-2-30-1 (1nb), S Watson 3-3-0-1.
Batting time: 212 mins. Overs: 48.
Umpires: Marais Erasmus (RSA), Kumar Dharmasena (SRL).