In reply to the home team's first innings total of 385, the tourists were 91 for two at tea, with captain Alastair Cook on 42 and Kevin Pietersen yet to score.
Cook, trying to emerge from a form slump, had already had a life on three, when Steve Smith grassed a tough chance from the bowling of Ryan Harris.
The left-hander attempted to flick a ball off his pads, but instead got an outside edge and it flew to the left of Smith at third slip.
Cook and fellow opener Michael Carberry rode their luck a little as they built a good opening partnership, with the latter also coming perilously close to being caught on two occasions.
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But together they blunted the pace of Mitchell Johnson and closed in on England's first century opening partnership in 12 Tests.
Just as that milestone loomed, Harris achieved the initial breakthrough, when Carberry dragged a ball back onto his stumps as he attempted to withdraw the bat with England on 85.
Root was adamant he hadn't snicked the delivery and immediately challenged the decision, but the replays were inconclusive and umpire Marais Erasmus's initial verdict stood.
Australia will regain the Ashes with a win in the third Test in Perth after going 2-0 up in the series with victories in Brisbane and Adelaide, and Smith's second Test century was the backbone of the home team's first innings.
He eventually fell to a DRS decision after getting an inside edge through to wicketkeeper Matt Prior from a Jimmy Anderson delivery, with Erasmus initially giving him not out.
Australia resumed at 326-6 and the day started well for England, with Stuart Broad (3-100) claiming the wicket of Johnson, who had not added to his overnight score of 39, with the second ball of the day.