The driver was not hurt and has been arrested on suspicion of driving under the influence.
Muni employees saw it happening, but they didn't believe it.
"When we did realize what he was doing - it was like 'no it can't be, not this morning.' And he went in," said Muni employee Tyrone Julian.
An SUV going about 40 MPH went into the Muni tunnel at Church and Duboce just before 6 a.m.. Employees stopped trains and ran in after it. The crashed SUV ended up about two city blocks deep within the portal. Julian said the driver appeared to be drunk.
"The only thing he said was: 'I'm not from here,'" said Julian.
Transportation officials had to shut down the N line in both directions while the cleared the tracks - creating a mess for morning commuters.
"They will get it all squared away. It's just not going to be snappy. This is one of those days where I will just have to make do," said Muni passenger Chris Jones.
Making do was not easy. There were buses to shuttle around the mess, but getting a spot on the buses was tough.
Muni has had problems with people accidently trying to drive into the tunnel before. It even happened this morning, crews dealing with the mess shoed a confused passenger away from the tunnel. Electronic signs have been put up to warn people to stop, but obviously it didn't work this morning.
"In my 20 years I have never seen anyone go in the tunnel like he did and go that far," said Julian.
Crews will wait till after midnight, when service has stopped, to remove the SUV from the tunnel. Right now the vehicle has been shoved to the side. A switch was damaged, so trains going into the tunnel will have to move slowly. Repairs to the switch will also be made overnight.