The motorway had been shut in both directions between the Lisburn/Saintfield turnoff and Stockman's Lane.
Army bomb experts were sent to the scene in the early hours due to the alert.
Police later said the alert had been triggered by a stolen vehicle which was found abandoned in the Lisburn area.
A number of diversions had been put in place.
Both lanes have since re-opened.
Motorists took to Twitter to vent their anger over the serious disruption, which caused serious delays for those travelling into the city.
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