It was lowered into the loch during its five-day tour round Scotland but failed to find any sign of a heartbeat in the murky depths.
However, organisers reported seeing "something pretty weird" as the baton neared the surface.
The search for Nessie has baffled monster hunters for years.
Reported sightings date back to the 7th Century, when a water beast is said to have appeared before St Columba.
Films, photographs and eye-witness accounts have all been offered as evidence of the creature's existence down the years, but definite proof has remained elusive.
The latest attempt to find the monster in the depths of Loch Ness took place on Sunday.
The Jubilee baton, which contains a device that can detect a pulse rate, was lowered 220 metres to the bottom of the loch from a boat.
Images of the baton underwater were beamed onto screens aboard another vessel, the Jacobite Queen, which was carrying about 100 guests.
Event director Di Henry said there was "a strange interruption" as the baton neared the surface again.
"There was a thing in front of the camera," she said.
"It looked pretty wooden. It could have been wood or seaweed or it could have been Nessie."
And she added: "I'm not so sure we didn't see something.
"It was pretty weird what we saw. I wouldn't want to overstate it, but it wasn't something I expected myself."
The baton arrived in Scotland on Saturday morning as it continued a 58,000-mile journey which has already taken it through more than 20 Commonwealth countries.
Starting in Stranraer, it was carried around the west of the country before ending the day in Glasgow - then making its way north on Sunday.
It will pass through a total of 78 villages, towns and cities across Scotland, being carried by hundreds of runners including politicians, celebrities and members of the public.
The baton started its journey at Buckingham Palace in March and will arrive in Manchester on 25 July for the opening ceremony of the Commonwealth Games.