The instructions below works for untethered iOS 4.3.1 jailbreak with PwnageTool 4.3 which is released by iPhone Dev Team for Mac.
Warning: Users who rely on Ultrasn0w unlock must stay away from iOS 4.3.1 jailbreak.
Untethered iOS 4.3.1 Jailbreak with PwnageTool 4.3
Launch the downloaded PwnageTool 4.2, and click OK button on its pop-up window
Chose Expert mode, click on your iDevice and click blue arrow button to proceed next
Click on Browse for IPSW… to select your downloaded original iOS firmware and click blue arrow to go next
On next window click on General option and click blue arrow button for next
iPhone users must check mark the box followed by Activate the phone option if they are on unofficial carrier, otherwise leave it as it is and proceed
Click blue buttons display on windows until you arrive to the window where you have selected General option, and this time click on Build option there
PwnageTool will ask to select a destination to save custom iOS 4.3.1, so provide that and click on Save button
PwnageTool will start building IPSW and during the process it asks for admin password, so provide that and click OK
On completion of IPSW building process, PwnageTool prompt to attach your iDevice to system, and it detects your device
PwnageTool will instruct you to put your iDevice into DFU mode, so follow the on screen instructions carefully to do that
Once your iDevice entered successfully into DFU mode, a message will display and iTunes will pop-up
In iTunes hold Alt key and hit Restore button and from pop-up window browse to your recently created custom iOS firmware and let it complete the restore process which may take about 10 minutes
Once done, you successfully jailbreak iOS 4.3.1 firmware with PwnageTool 4.1.