The pair drifted some distance but eventually managed to get ashore.
They were taken to Tauranga Hospital suffering from hypothermia.
A man and a woman in their 30s, and a man in his 40s, were in the two vehicles left on the bridge. They were taken to hospital with moderate injuries.
The driver of the submerged vehicle was still unaccounted for and the police national dive team would be travelling to Tauranga to assist.
Inspector Steve Kose from police northern communications centre said the submerged vehicle appeared about four to five metres underwater in the middle of the channel, he said.
TECT Rescue Helicopter, Tauranga Coastguard, police and fire crews were all at the scene tonight.
There is no reports of injury in relation to the other vehicles as this stage, but two people were being treated for possible hypothermia, that included the passenger in the submerged vehicle.
Maungatapu Bridge is closed to all traffic and motorists are asked to avoid the area.
Maungatapu resident Mikki Uden said it appeared a car travelling northeast had swerved onto the wrong side of the road and smashed through the barrier into the water.
The car was not visible and emergency services, including boats, were out looking for it.
She did not know whether anyone had been rescued.
"The harbour's really deep here and the tide's coming in.''
Another Maungatapu resident, who did not wish to be identified, said traffic had been backed up for miles in both directions for about an hour, but had since been cleared.
It was not the first time a car had gone off the bridge, she said.
"There's so many accidents on that bridge, I don't know why. Whether people are looking away at Tauranga in the distance, or something going on in the water, I don't know.''
Do you know anything about the crash? Email newsdesk@nzherald.co.nz.
