The card is backwards compatible so, yes, it'll be perfectly fine. The difference between the two is mainly the bandwidth and speed for data throughput and you won't likely notice a difference. Here's a bit of info:
Summary of PCI Express Interface Parameters:
Base Clock Speed: PCIe 3.0 = 8.0GHz, PCIe 2.0 = 5.0GHz, PCIe 1.1 = 2.5GHz
Data Rate: PCIe 3.0 = 1000MB/s, PCIe 2.0 = 500MB/s, PCIe 1.1 = 250MB/s
Total Bandwidth: (x16 link): PCIe 3.0 = 32GB/s, PCIe 2.0 = 16GB/s, PCIe 1.1 = 8GB/s
Data Transfer Rate: PCIe 3.0 = 8.0GT/s, PCIe 2.0= 5.0GT/s, PCIe 1.1 = 2.5GT/s
Taken from the following:
http://www.trentonsystems.com/applications/pci-express-interface