The small fire, apparently mechanical, was quickly put out and there were no injuries.
However, it disabled the bus and smoke spread through the south tube of the tunnel.
Traffic, including other buses, was able to drive around the bus, which was disabled in the left lane.
There were 60-minute inbound delays at the tunnel as a result.
The Port Authority says it was a minor vehicle fire, possible caused by leaking oil. The bus driver put it out and the bus was towed out of the tunnel's center tube.