You can simply say that "she and he are in your thoughts".
You can give condolences and be honest.
I'd them that I'm sorry for their loss, that they'll be in your thoughts and that I'll help any way I can / here if they need anyone to talk too. Offering the reassurance that she is no longer has to suffer may help too. They may take these statement/offers in a religious context. But you can't do anything about that, plus you actually offered non-religious thoughts so you can rest assured that you also weren't hypocritical.
Atheists face death and loss just like all other people. Sure, we may disagree with theists on what happens after death, but that doesn't mean that death itself isn't a shared human experience. Most of us -- not as atheists, but rather as fellow human beings -- have thoughts and feelings on loss, and we have sorrow and sympathy for those who are grieving.
I think, if you focus on your feelings toward this person and his girlfriend, there's probably some religiously neutral sentiment you can voice. In terms of things you can offer other than prayers: sympathies, condolences, thoughts, some kind words... take any compassionate feeling you have towards this person in his time of need and try to express it honestly.
Hi Tianna and welcome to TA! You will find these and other types of advice questions are welcome.
I agree with what others have said. You can say "you and your family and in my thoughts and if there is anything I can do please do not hesitate to ask". You can be very clear in your empathy while at the same time not feel like you are selling out.