One form reports a contribution to an account and one form reports an additional tax on a distribution from an account. Form 5329 reports additional taxes on qualified plans, including individual retirement arrangements (IRAs) and health savings accounts (HSAs and MSAs). If you owe an additional tax--for example because you took an early distribution from an IRA--you'd include Form 5329 with your tax return. A 5498 is an informational form that you should store with your tax records. Your financial institution sends you a Form 5498 when you contribute to an IRA (or a 5498-SA when you contribute to an HSA or MSA).
Note: The "-T" at the end of 5329 means the form is for the person listed as the taxpayer on the return. A "-S" would indicate a form for the person listed as the spouse on the tax return.