Thank you for your question. My apologies for the delay in response.

Because I don't know exactly what recipe you are using, I don't know how much vinegar your recipe called for...however the National Center for Home Food Preservation Chile Salsa II recipe calls for 1 cup of 5% vinegar in the 6-8 pint batch. 

Assuming that is similar to your recipe, if the vinegar was left out we cannot be sure the finished product has a low enough pH to inhibit bacterial growth in the processed jars.  I would recommend that you mark the jars without the vinegar, store them in the refrigerator and use them within a month or two.  You could also freeze the salsa for longer storage.