Match referee Ranjan Madugalle subsequently fined Ponting 40% of his match fee. He could have been banned for the final Test in Sydney, but received a lesser punishment."Ricky's actions as captain of his country were unacceptable," the Sri Lanka said in a statement. "A captain is expected to set the example and not get involved in a prolonged discussion with the on-field umpires and question their decision.
"While pleading guilty to the charge, Ricky understood that the discussion went far too long. He apologized for his action and stated that he has nothing but respect for the umpires and his on-field actions were not intended to show disrespect to Aleem Dar or Tony Hill."
It was the latest setback for Ponting, who went into the match nursing a fractured finger which has hampered his fielding, and he failed again with the bat as Australia made just 98 in Sunday's opening sessions.
England resumed on 157-0 but soon lost Alastair Cook as the left-hander added just two runs to his overnight 80 to become the first of Peter Siddle's three victims.
Siddle then dismissed captain Andrew Strauss for 69, but Trott and Pietersen added 92 for the third wicket.
Pietersen was on 49 when the controversy struck, but although he survived to make his 21st half-century in 70 Tests the South Africa-born player did not last much longer as Siddle trapped him leg before wicket for 51 with a low delivery.
Trott also had some luck before reaching 50, having apparently been run out from Ponting's throw before video replays gave him the benefit of the doubt.
Mitchell Johnson continued his revival of form which saw Australia level the series at 1-1 with victory in the last match in Perth, as the left-arm paceman had Paul Collingwood (8) and the in-form Ian Bell (1) caught hooking at short deliveries.
Johnson thought he had Matt Prior out as well when the batsman was on just six, but a replay called for by Dar showed that he had bowled a no-ball.
Prior then helped Trott add an unbroken 158 for the sixth wicket as England reached stumps on 444-5 for a lead of 346 runs with three days still to play.
Trott scored his third century in five Ashes appearances and his fifth in 17 Tests overall as he ended the day on 141, having hit 12 fours off 278 balls faced.
Prior, like Trott also born in South Africa, took toll on the Australian bowlers as he smashed 10 fours in his 75 from just 105 deliveries.
Victory in Melbourne will mean that England retain the Ashes urn no matter the result in the Sydney finale starting on January 3