The army bomb squad was called after an abandoned car was reported near the Blacks Road off-slip just after 2am on Monday.
Diversions were in place for most of the morning, including rush hour.
Following examinations police revealed that the car, which had earlier been reported missing in the Lisburn area, did not contain any suspicious objects.
A statement confirmed: "The vehicle was reported stolen in the Lisburn area. Nothing untoward was found in the vehicle that has been taken away for further examination."
The alert is now over and the motorway has been reopened in both directions.
At the height of rush hour, traffic heading into the city was tailed back as far as Lurgan, while the disruption also had knock-on effects on many minor routes around the road closures.
There was also a separate security alert on the Westlink earlier, which similarly ended after police found "nothing untoward" in the area.
The alerts are the latest in a series of incidents this month - 14 in the Belfast area alone.
Local business leaders said it is causing misery for shoppers and staff trying to get into work, and is having a bad impact on the Northern Ireland economy.
"Small traders who have only four of five staff are particularly hard hit by this type of idiotic hoax," explained Glyn Roberts of NIIRTA.
"We are fast approaching the Christmas shopping season and given the events of last year, this disruption is the very last thing struggling City Centre Traders need.
"The sooner those behind these hoaxes are caught and convicted, the better for all"
Local SDLP councillor Tim Attwood said dissidents will not succeed.
Mr Attwood said: "It is clear that this traffic chaos is hitting commuters and business hard. However the message is plain, the IRA did not succeed in their bombing campaign and dissidents will not succeed either.
"The reality is the overwhelming majority of people are opposed to their activities and want to see a more prosperous and peaceful Belfast."