Police said it was part of an investigation into dissident republican activity.
A number of roads were closed, including part of the Westlink between 21:40 and 22:15 GMT.
Army bomb experts attended the scene and carried out searches. The alert ended shortly after 02:00 GMT.
The car was taken away for further examination and residents were able to return to their homes.
North Queen Street Community Centre had been made available for them during the alert.
"I would like to thank motorists and the local community for their support while we dealt with this situation," Ch Supt Chris Noble said.
"I understand the disruption that this caused to a lot of people and we appreciate the patience and understanding shown by residents as we focussed on ensuring their safety."
A number of people were moved from their homes in north Belfast on Saturday night while police examined a "suspicious vehicle" at Plunkett Court.