You will be fine even if it is PCI-E ver. 2 which I think it is. PCI-E ver. 3 has more bandwidth but no GPU even out now will use all of the bandwidth of PCI-E ver. 3 so you will be fine. The think I would worry about is the 350watt PSU in that system is on the low side. And most of the pre-built system only put in PSU's just large enough to handle the power of the system as it comes from the factory.
like bryonhowley said, your PSU is your down side. Nvidia recommends atleast a 400 watt psu. with this 350 watt PSU you maybe JUST able to run the 650 ti. i suggest upgrading the PSU to atleast 400 watts.ive calculated and found that your power consumption would be about just over 300 watts on load. so your 350 watt PSU will hold it but i still recommend getting a 400 watt PSU.