To answer the actual question, there is no way to update a PCIe 2.0 motherboard to 3.0. Some motherboards will let you choose which version to use for particular slots in the BIOS, but it is not possible to run a version newer than the motherboard originally came with.
That said, as mentioned already, PCIe versions are backwards compatible so far, so the card will work fine. There is no graphics card I know of that fully saturates PCIe 2.0 x16 when gaming, either, so performance should not be affected.