Yep, 2.1 is a very minor change and all PCI-Es are designed to be backward compatible.
As you can see from wiki:
PCI Express 2.1 supports a large proportion of the management, support, and troubleshooting systems planned to be fully implemented in PCI Express 3.0. But, the speed is the same as PCI Express 2.0.
Very little difference.http://en.wikipedia.org/wiki/PCI_Express#PCI_Express_2.1