The jury was shown images of Malkinson and Quinn from around the year of the attack, as well as a police e-fit image that had been produced in 2003.
Price said the assault must have been carried out by someone who knew the area.
“He was not only a local man, he was also someone who knew of that obscure location,” he said.
“A man with prior knowledge of its existence and accessibility, someone who, as he followed her over that distance as he did, knew she was soon going to reach it and so timed his attack upon her precisely to coincide with her passing close to somewhere he knew he might easily, forcibly and swiftly take her out of sight and away from the road.”
The jury was told Malkinson, who worked at the nearby Ellesmere Shopping Centre, became the prime suspect within hours.
He was originally linked to the crime by two police officers who had stopped him on a motorbike a few weeks before the attack and thought he resembled the e-fit of the suspect.
However, Price said that when police spoke to Malkinson the day after the attack, he had no sign of a scratch to the face that the victim had recalled inflicting as she struggled.
At the time he lived with a friend in a flat in Little Hulton, around a mile-and-a-half from the scene of the attack.
Six days after the rape, Malkinson, who had been having problems with people who he had previously lived with, abruptly quit his job and left, telling a friend he was going to Holland.
This sudden departure prompted police to track him down to a Salvation Army Hostel in Grimsby, where he was arrested and brought back to Salford to attend an identity parade.
Price told the jury: “The identifications of [Malkinson] were all honestly and genuinely made but, we submit, mistaken.
“As anybody’s own personal experience shows, it is easy to do, even with someone you know.”
He added: “Evidence gathered in the second investigation, including DNA evidence, and which will be put before you in this trial, proves, it is submitted by the prosecution, that it was Paul Quinn and not Andrew Malkinson.”
The trial continues.