The trial is being held under heavy security
The e-mails, sent to news organisations following Pearl's disappearance in Karachi on 23 January, carried a picture of him in captivity with a gun held to his head.
Chief Prosecutor Raja Qureshi told journalists on Wednesday that witness Sheikh Naeem, an internet service provider, had confirmed that one of the accused, Fahad Naseem, sent the e-mails using his network.
Mr Qureshi said another witness had identified Mr Naseem and co-accused Salman Saquib as the buyers of a polaroid camera which police say was used to photograph Mr Pearl in captivity.
A third witness, who works for a telephone company, is said to have verified that the accused men made calls allegedly about the American journalist's abduction.
Mr Qureshi made his comments outside the closed-door trial in the southern city of Hyderabad, where the trial is being held amid extremely tight security.
FBI's help
His remarks follow testimony on Monday by another witness who, after examining handwriting, said prime suspect Sheikh Omar could have drafted the e-mails.
Sheikh Omar and the other three defendants have pleaded not guilty to charges of terrorism, kidnapping and murder.
Mr Qureshi and his colleagues say Sheikh Omar masterminded Pearl's abduction while the other three accused carried out his instructions.
An investigator from the American FBI explained to the court on Saturday how he had traced two incriminating e-mails to Fahad Naseem's laptop computer.
Pakistani police say Mr Naseem then implicated the other suspects.
Blasphemy charge dismissed
The e-mails protested at alleged ill-treatment of prisoners captured by US forces in Afghanistan, accused Mr Pearl of being a spy and threatened to kill him.
Later, a video cassette purporting to show Mr Pearl's throat being slit was sent to US diplomats in Karachi, although Mr Pearl's body has not been found.
On Tuesday the video was shown to the court and defence counsel said it was a fake which had been made with the aid of computers.
The defence also filed charges of blasphemy against Chief Prosecutor Qureshi, which the anti-terrorism court dismissed on Wednesday.
Sheikh Omar's lawyer, Abdul Waheed Katpar, said the special court's decision could be challenged in a higher court.