Yes it will. Physically, both are x16. The 2.0 and 3.0 are version or speeds. They are backward compatible (like the USB2.0 and USB3.0).
Plugging a PCIe3.0 x16 GPU on a PCIe2.0 x16 slot will run the GPU on 2.0 speeds (and vice-versa). Though it is "slower", it is not noticeable in real-world usage.