It is possible to replace the Airport Express card on a Mac Pro. I haven't been able to find any information about how it is supported. My understanding is that it isn't considered by Apple as a user upgradable option.
Technically, the way an add-in card wakes the system is via a wake signal which connects to the slot. PCI and PCIe slots have this connection, called PME# and WAKE# respectively (the # means it is asserted when low or close to 0V).
It looks like the slot (labeled FOXCONN 682WD )in a Mac Pro is or is related to the mini PCI slot, which are typically found on laptops. If this is the case, then there is a good chance that a newer add-in card could also work in an older system and be able to wake the system.
There is risk that a card meant for a newer Mac Pro won't fit because the cards may be specifically designed for the one system they go in and have some sort of mechanical interference, such as a big capacitor, even though the slot is the same.
BTW, here is the information from my white MacBook which is similar to the article linked above but with newer firmware and 0x88 at the end of the Card Type instead of 0x1367.
Card Type: AirPort Extreme (0x14E4, 0x88)
Firmware Version: Broadcom BCM43xx 1.0 (126.96.36.199)
Wake On Wireless: Supported