The airport tweeted just before 11:30 p.m. NT that flights should be able to arrive shortly.
Around 8:30 p.m., the airport had tweeted it had shut down air traffic due to a bomb threat.
The Royal Newfoundland Constabulary said early Friday morning that the bomb threat was found written on a note found on the Air Canada plane bathroom before it left the gate.
Police interviewed three St. John's women who had used the facility, but all three were released.
Overall, the bomb threat affected 13 flights headed in to St. John's.
Notified of threat
Air Canada flight 143 scheduled to depart St. John's for Ottawa at 6:50 p.m. was notified of a possible bomb threat on board the aircraft as it was pulling away from the gate, the airport authority said in a release.
The Embraer 190 carrying 82 passengers and four crew members was safely evacuated.
RCMP, the Royal Newfoundland Constabulary, St. John's Regional Fire Department and Eastern Health all responded to the incident, along with the authority's emergency response team.
The departures lounge at St. John's International was also evacuated, and no other aircraft was permitted at the terminal building until it was cleared.
Stuck on the runway
Following the airport's announcement that air traffic would resume, passengers waiting in the airport applauded when the first check-in was announced.
The lineup to get through security to board flights stretched through the airport around midnight Thursday.
Around 11 p.m. NT, the airport started handing out $5 vouchers to stranded passengers so they could get food.
Meanwhile, passengers on board other flights remained on the tarmac, with some people tweeting they were sitting waiting on a plane for two hours.
Erin Normandeau, who was on a United Airlines flight from Newark to St. John's, said her flight arrived at 8:15 p.m., but was stuck on the runway with passengers unable to depart.
"Even the pilot was like, 'I don't even know what's happening,'" she told CBC News earlier Thursday evening.
The pilot of her flight announced passengers should be able to de-board the plane by 10 p.m.
However, passengers on the United Airlines flight were told around 11 p.m. it would be roughly another hour and a half before they would be allowed off the plane.
Family members of a passenger told CBC News the pilot of the Air Canada plane involved in the bomb threat issued an alert over the aircraft's intercom saying they needed to do a "rapid evacuation."
The family said passengers were unable to take any items off the plane with them, only what they were wearing.
According to the family, the passenger aboard the plane wasn't able to even take her purse with her.
Multiple flights headed for St. John's were diverted to other parts of the island due to the threat, including Gander International Airport.
Some passengers who were destined for St. John's but wound up in Gander decided to get together and rent a car to get to the city.
Passenger Wayne Hiscock was flying in from Happy Valley-Goose Bay to St. John's when the bomb threat prompted his flight to divert to Gander, but his wife decided to drive out from St. John's to pick him up.
Meanwhile, some other passengers were left to wait in the Gander terminal for updates on their flight.