If it's a verbal warning then there's no permanent record. Check your companies disciplinary procedures. It's doubtful that they can issue what is effectively a written warning without 1st issuing 1 or 2 verbal warnings. Get this sorted through your HR dept. If your manager isn't following the procedures the HR dept are usually pretty keen to sort it out!
FYI, the employer doesn't have to issue any verbal warnings, they can go straight to written or final written.
I agree that a formal warning is a bit harsh for this but you don't say how late you were, if you called to say you would be late or apologised as soon as you got in the door.
If an employee of mine was late, say by an hour, didn't call to say they were on their way & I had to confront them when they did turn up, I would probably issue a written warning too.