My son's tuition is paid through Federal student loans (from the FAFSA program). Can we enter the tuition paid on our joint tax return because he is a dependent? We did not actually pay any tuition though, it was all covered through loans. We did pay for his books though.

The books should be covered but I don't know about the FAFSA.

No student loan is not deductible. If you paid interest on the loan, then student loan interest is deductible.