Electrical – DS3231 Real Time Clock i2c 3volt battery 5V arduino

I've solved problems like that in the past with a Sziklai pair. It's like a Darlington, but with two complementary transistors. In your case, use a PNP transistor with its emitter connected to the alarm chip's VCC, and the base, through a resistor, to the open drain alarm output. The collector goes to the base of an NPN transistor (again, through a bias resistor) wired as a low-side switch for your 9 volt circuit.

I suggest you get a I2C compatible bi-directional buffer with tri-state/high impedance mode using "ENABLE" style signal.

I found one by NXP called the PCA9517A (which is on digikey for $1.37 a piece or 59c in bulk) which does all of the above, plus allows for voltage level shifting and defeats bus capacitance issues! The same signal used to remove power from the RPI can be used to drive the enable pin, thus detaching that whole side of the I2C bus from the AVR's side.

Another note about the PFET circuit you show - you need a logic-level gate voltage PFET, and you need to use a BJT to properly turn the PFET on/off, and at least put the pull up resistor there.

It should look more like this to operate correctly:

^{simulate this circuit – Schematic created using CircuitLab}

Please realize that the capacitors I show are very important, the RPI needs good power supply decoupling and heavy duty bulk capacitance nearby, I suggest you place the capacitors as close as you can to the RPI's 5V input.