The mobile phone company had threatened to recommend the rest of the Virgin Group pulled ads from all News International papers - a move that could have cost Murdoch's business millions in lost advertising. Last year, Virgin Mobile alone spent £1.9 million on advertising with The Times and The Sunday Times.
Virgin issued the warning after The Times rejected an ad challenging its rival Orange's earlier "fair rates" campaign.
The Virgin response was due to run a day after Orange purchased all the advertising space in Friday's sponsored edition of the paper at an estimated cost of £250,000.
But a truce was reached following an emergency meeting between newspaper executives, Virgin Mobile and its media buying agency, Manning Gottlieb OMD.
Virgin, which withdrew all its ads from last Monday's edition of the broadsheet, subsequently resumed advertising, while The Times agreed to run the controversial ad later this week.
The mobile operator accused The Times of seeking to protect its commercial interests with Orange and indicated its intent to take the issue up with the IPA and ISBA.