If your W-2 is wrong, you need to get it corrected by your employer. There is no other way to deduct 401(k) contributions.
Box 1 is your wages subject to income tax. Any pre-tax deductions, such as retirement contributions and medical insurance premiums, should be subtracted from your gross pay and not included in box 1. Certain pre-tax items are also exempt from sosicsl security and Medicare tax but not retirement. Usually with 401 contributions, box 3 and 5 will be higher than box 1 by the amount of the retirement contributions. (Although amounts contributed by your employer are not included in box 1, 3, or 5.)
It sounds like you need to get a corrected W-2 before you can file.