OK, I've just looked at the schematics and it is not exactly the same design as yours. For mine :
there is a pushbutton that allows a contact between PWRKEY and PWRKEY_OUT (pins 1 and 2 of sim900) , in the case you want to start it manually . The PWRKEY pin goes on the colector of a npn transistor , its emitter wired to GND, and its base goes to D9 (so, also arduino D9 ) through a series resistor . When D9 is put to HIGH, the PWRKEY pin is grounded via the transistor.
AMHA, you could use the same design to drive the PWR pin, thus you can control the current on your PWR pin (maybe with a little resistor), and you are sure you won't put too high voltage on this pin .
Here is the schematics of the one I use http://www.seeedstudio.com/wiki/images/3/32/GPRS_Shield_V2_Schematic.pdf