Here are some important points to note about the difference between both documents: In their simplest form; A Cover Letter as the name implies, can cover any kind of document--a report, a CV/résumé, a budget, application package, even an application letter!, while an Application Letter is specifically an application for seeking a job.
An application letter is often intended to stand on its own, and basically contains your qualifications and describes a bit of who you are and what you have done, as well as, your objectives and why you want to apply for a job.
Whereas a cover letter generally can't be the applicant's only document submitted to express interest in a job opening. A cover letter typically accompanies each resume you send out.
A cover letter should complement, not duplicate, your resume. Its purpose is to interpret the data-oriented, factual resume and add a personal touch.
A Cover Letter is usually a page you have typed in the format of any buisness letter in which you introduce yourself to a perspective employer.
While an Application can sometimes be a form that is given by a hiring company or person in which you would fill in information asked for on this form that would often be included in a resume. Many employers will ask you to write to them perhaps in the form of application letters when they advertise jobs. Sometimes you will be asked to send your CV or resume. Your CV or curriculum vitae lists your educational and career history and is a useful summary for an employer of all your educational and employment achievements up to the present time.
You must always ensure that it is up to date. A covering letter may then be very useful because you can enclose it with your CV or the completed application letter. In your covering letter you can then draw attention to particular information which you wish to highlight in the other documents it covers (application letter or CV). Finally, however, to clear your doubts, cover letters can also sometimes be used as application letters.