Before the jury was brought in to hear the opening arguments in Baltovich's retrial, Crown attorney Philip Kotanen said the prosecution could not proceed due to a lack of evidence.
"There is no longer any reasonable prospect of conviction," he told Superior Court.
Defence lawyer James Lockyer said Baltovich's defence team collected evidence that doesn't prove beyond a reasonable doubt that serial killer Paul Bernardo murdered the 22-year-old, but does raise a "reasonable possibility" and "including the probability" that Bernardo committed the crime.
Justice David McCombs directed the jury to acquit, saying the only verdict
that could "be supported in this case" is not guilty.
This was the second trial for Baltovich in case of the disappearance and death of Bain.
Baltovich, now 42, spent eight years in jail before Ontario’s highest court quashed the conviction and ordered a new trial. During the appeal, his lawyers argued that convicted killer Paul Bernardo may have murdered Bain, whose body was never found.
The 22-year-old student at the University of Toronto's Scarborough campus disappeared on the afternoon of June 19, 1990 after telling her mother she was going to the campus tennis courts.
Three days later her car was found two blocks from the campus with a substantial quantity of her blood in the back.
Jurors also heard that her body has never been found. Baltovich was first charged with her murder in November 1990.