I had this happen twice with my YJ. Once it was the alt. the other time the terminals.

Check all your connections to the charging system. Grounds, positives, the little wires with the clip connector (I actually bought a wrecking yard alt once and when removing found out the clip was broken and the connector was just moving out of place causing the system to stop working)make sure to check everything so you don't waste money like I have.

If that fails get your alt tested.