Detective Chief Inspector Jackie Sebire said “two minor components of another contributor’s DNA” were found on the zip toggle and padlock.
The evidence came to light as she appeared to rule out that Williams got into the bag himself.
Relatives of the MI6 spy want to know if he was killed by secret services.
Family members fear “some agency specialising in the dark arts” may have been involved in a cover-up that leaves them with no way of knowing how and why he died. Relatives believe someone was either present when he died or broke into his home afterwards to destroy evidence.
Sebire told Westminster Coroner’s Court: “My thought, or my opinion, since I went into the scene is that a third party had been involved in the death or by putting the body in the bag. So my primary focus was looking at the bathroom.”
Video of the immaculately kept flat at the centre of Williams’ death riddle showed a cutting from the Observer newspaper headlined “top five regrets of the dying”.
The video took the inquest on a walking tour of his Pimlico home, showing a woman’s red wig, lipstick, and make-up, in the condition that it was found.
Footage then showed close-up images of the bathroom suite where Williams’s body was found.
The film zoomed in on the red North Face bag, showing bulges from his limbs inside and a brass padlock locking two zips together from the outside.
Williams was found in the foetal position in the bag, there were no signs of struggle and his body position appeared “calm”, Sebire said.
Sebire said she would have expected to find fingerprints left by Williams on the bathroom tiles.
“Certainly there were no prints of anybody’s in the lower-tiled wall,” she added.
Williams had not damaged the bag or sustained injuries to his hands, the detective said.
“He was very muscular, he trained regularly. I would at least expect some tearing to the netting.”
Sebire said she allowed a counter-terrorism officer from SO15 into the flat. But she said she was solely responsible for investigations into the death.
Williams’s sister, Ceri Subbe, sat in the hearing without her parents as images showed the scene which greeted detectives as they arrived at his flat on Aug 23, 2010.
There was no sign of a break-in at the flat, with footage showing Williams had left cash in a cupboard and a mobile phone on the living room table. There was little clutter in the flat except for a dressing gown and quilt discarded on the bedroom floor.
The inquest continues.