Polemics have been flying since 18-year-old striker Mario Balotelli, who scored twice, helped league leaders Inter come back from 3-1 down by converting a penalty after going down in the area.
Roma coach Luciano Spalletti and midfielder Daniele De Rossi said after the match that Balotelli had dived and Juventus boss Claudio Ranieri, whose team trail Inter by seven points in second place, sided with them on a television show.
"I don't like intellectual prostitution. I like intellectual honesty," Mourinho told a news conference. "There has been great intellectual manipulation over the last few days. A great job has been done to manipulate public opinion.
"Over the last two days we have not talked about a Roma side with great players, lots of players I wanted to have with me, that will finish the season with zero titles.
"We have not talked about Milan, who will finish the season with zero titles. We have not talked about Juventus, who have won lots of points with refereeing mistakes.
"You cannot say it was not a penalty, you can say there is a doubt," said Mourinho, who frequently courted controversy during his three-year stint at Chelsea.
TV replays did not clearly show Balotelli making contact with a Roma player, nor did they prove he deliberately tumbled, although the Italian media were united in saying the referee made the wrong decision.
Mourinho's comments sparked a swift response from Juventus.
"Juventus expresses shock and indignation and asks Inter to disassociate itself publicly from these comments," the Turin club said on its website.
"With his statements Inter's coach lacked respect not only to Juventus and its 14 million fans, but (also) to the whole of Italian soccer."
Instead, the Serie A champions backed their coach, saying in a statement:
"Jose Mourinho responded in a clear, explicit way to an attack of the same level. Our coach expressed his ideas, without insinuations, without malice, according to his style, which is much appreciated by the club."
Inter and Juve's already fierce rivalry worsened in 2006 when Juve were stripped of the title and demoted in a match-fixing scandal as Inter became champions and signed Zlatan Ibrahimovic and Patrick Vieira from their rivals.
