Employer Student Loan Repayment Alternate Tax Level

My employer offers a student loan repayment plan where they make yearly payments directly to the student loan servicer. It is a qualifying educational assistance program however my employer has set the tax-free limit at $3,000 instead of the IRS allowed $5,250. If for example I they make a $5,000 payment they will add $2,000 ($5,000 minus $3,000) to my taxable income and my next paycheck will reflect the additional taxes.

 

When I file my taxes this year is it possible to subtract that $2,000 from taxable income since under the IRS guidelines it would qualify as tax fee?