Joan Aitken, the Traffic Commissioner for Scotland, said she had found no evidence pointing to failings by the Carluke-based company over the crash on the A73 near Biggar.
Ms Paton, 17, was killed and 32 others injured among a Lanark Grammar School group en route to Alton Towers theme park in Staffordshire when the coach crashed off a bridge in icy conditions.
Last year, a sheriff found coach driver Raymond Munro was at fault for the crash by travelling too fast for the wintry conditions.
Sheriff Nikola Stewart also said the girl might have survived had she been wearing her seatbelt.
The firm was called to yesterday’s public inquiry following investigations by the Driver and Vehicle Standards Agency.
Ms Aitken said she was told during the hearing the company’s vehicle maintenance standards were satisfactory with minor shortcomings.
She said: “The Driver and Vehicle Standards Agency evidence did not point to fault on the part of the operator in the lead up to the crash.”
She issued a warning about some of the “further improvements required” by firm, but said that these would not have prevented the crash.
Ms Aitken granted a new licence to James and Kenneth Purdie to operate as a limited company rather than the previous partnership.
A spokesman for Ms Aitken said Mr Munro had not appeared before her “because he no longer holds an entitlement to drive buses or coaches”.