What is meant by the expression I enjoyed your company?

The Word company here means companionship, or the traditional meaning of "having company". I enjoyed your company means that I liked spending (this specific) time with you (on this occasion. It is a more formal manner of speech than we use today, and was primarily used between a suitor and a young lady who had spent time on what we now call 'a date'. But a group could also enjoy each other's company.