Samuel Beattie, 47, was arrested at his Mount Macedon home in Victoria on Monday morning and charged over the attack in St Albans in Melbourne's west in 1996.

It's alleged Beattie broke into the home of the then 39-year-old woman and attacked her in the early hours of July 23.

The woman, a mother of three, died from cancer in 2006.

Beattie faced Melbourne Magistrates Court on Monday evening on two rape charges and one of aggravated burglary.

During a bail application, Detective Senior Constable Anthony Murphy said the victim had yelled "please don't hurt me" after Beattie broke into her home just after 5am.

He said Beattie told the woman he would't hurt her if she kept quiet.

"My name is John, I just want to make love to you," the detective said Beattie allegedly told the woman during the attack.

Beattie then told her "I'm sorry" before leaving the house, he said.

DNA samples were taken at the time. The officer said those were matched to DNA swabs taken from Beattie in an unrelated matter last year.

The results showed Beattie was 100 billion times more likely the source than any other person, he said.

The court heard Beattie was on bail for other matters, including reckless conduct endangering serious injury charges.

Police opposed Beattie's release on bail, saying he was an unacceptable risk.

But his lawyer Courtney Hart said he had no relevant priors and noted the allegations were historical.

She acknowledged he faced a significant prison sentence if convicted, but said he had a successful business and stable home.

But the magistrate noted a lot of Beattie's prior offences had been committed while he was on bail, and questioned what he'd done about what appeared to be a "substantial alcohol problem".

"He's shown a total disregard for the fact that he's on bail and has continued, allegedly, to commit further offences," he said.

"He has a shocking alcohol problem and you cannot illustrate to me that he is addressing that problem, and that puts him at the risk of further offending."

He refused to grant bail and told Ms Hart to come back with a treatment plan.

His case will return to court for a committal hearing on January 15.

Australian Associated Press