DFARS 232-7002 contains exceptions to the DOD policy of payment requests be submitted in electronic form.  Paras 4 & 5 state:  

(4) Cases in which the contractor has requested permission in writing to submit payment requests and receiving reports by nonelectronic means, and the contracting officer has provided instructions for a temporary alternative method of submission of payment requests and receiving reports in the contract administration data section of the contract or task or delivery order (e.g., section G, an addendum to FAR 52.212-4, or applicable clause); and

(5) When the Governmentwide commercial purchase card is used as the method of payment, in which case only submission of the receiving report in electronic form is required.

 Therefore, the Contracting Officer can grant an exception to a contractor unable to utilize the WAWF system.  

48 CFR contains language on exceptions to use of WAWF when contractors cannot submit  electronic invoices.  See Paragraph 7 of the following DFARS ruling from the Federal Register: 

  https://www.acq.osd.mil/dpap/dars/dfars/changenotice/2008/20080303/E8-3947.htm.  

7. Recommendation To Clarify Who Has Exception Authority (Procuring 
Contracting Officer (PCO) or Administrative Contracting Officer (ACO)) 
for Use of WAWF

    Comment: One respondent recommended clarification in the contract 
clause and its prescription to provide authority for the PCO to grant 
exceptions to the use of WAWF at the time of contract formation. The 
determination should be included in Section G of the contract, 
eliminating the requirement for a copy of the ACO's determination to be 
provided with each payment request.
    DoD Response: Prior to award, the PCO may authorize a contractor to 
use an electronic form other than WAWF, in accordance with DFARS 
232.7003(b), and the authorization will be annotated in Section G of 
the contract. After award, the ACO may authorize (in writing) the 
contractor to submit non-electronic payment requests and receiving 
reports when electronic submission would be unduly burdensome to the 
contractor (DFARS 252.232-7003(c)(3)). The requirement for the 
contractor to provide a copy of the ACO's written authorization with 
the payment request is intended to facilitate processing of the request 
and prevent inadvertent rejection of the paper document.