Australia were left fighting to get back into the fourth Ashes Test after being made to follow on by England on day three at Trent Bridge.
The visitors closed on 222-4 in their second innings, with Justin Langer making 61 and Andrew Flintoff (2-33) leading the home attack.
Australia's deficit stood at 37 runs, having been made to follow on for the first time since 1988 and in 191 Tests. Top bowler Simon Jones earlier took 5-44 as the Aussies were out for 218.
It was his absence from the field for a large part of their second innings which led to a row between Ricky Ponting, umpire Aleem Dar and the England players which could result in the Australian captain face punishment.
The Australian captain seemed to be angry that substitute Gary Pratt ran him out and pointed towards the England dressing room to challenge the absence of Jones, who was receiving treatment for a right ankle injury which led to him going to hospital for a scan.
Ponting said afterwards: "I was very disappointed with my dismissal given it was at a crucial stage of the game and I had worked very hard to get to that position.
"I no doubt let myself down with my reaction and for that I apologise to those who see me as a role model.
"My frustration at getting out was compounded by the fact I was run out by a substitute fielder - an issue that has concerned us from the start of this series and one that we raised prior to the series."
Ponting could become the first Australian captain since Allan Border in 1986-87 to lose an Ashes series.