A three-man panel eventually dismissed Heinze's argument that a letter signed by Red Devils chief executive David Gill - citing a fee at which a deal could be done - constituted an agreement to sell.
Liverpool boss Rafael Benitez was flabbergasted at the verdict, claiming he had been "100% certain" Heinze would end up at Anfield.
Ferguson labelled Benitez's remarks "churlish", then confirmed Gill is leading an inquiry into the way Liverpool have acted.
"We are looking at Liverpool's whole role in this," he said.
"We are not letting them off with it. That is what we are investigating."
Asked whether he was alleging Liverpool had 'tapped up' Heinze, Ferguson replied: "We will see how it comes out. David Gill is working on that at the moment. We will get to the bottom of it."
Ferguson was always confident the Premier League would back United's stance of not selling to Liverpool, or any of their major domestic rivals.
He was quick to hit back at Benitez's jibe that United enjoy favouritism in the drafting of the fixture list.
"It is disappointing stuff," said Ferguson.
"He talks about the fixtures. He should have seen our fixtures over the last two or three seasons.
"There was never any chance of Liverpool winning that case, so Rafa clearly did not read the Premier League rules. It is just churlish."