Hi, probably enough time with a few caveats...which rental car agency are you using? Will you need to refuel the car before returning it? Which airline? Do you have priority status with the airline (meaning you can use the shorter security screening line? Will you leave from the downtown San Diego area? From SD you will take the 5 North to the 405 N and Exit at Century Blvd. At the bottom of offramp, you will turn L and go under the freeway heading West towards ocean and head to the rental car lot.
All rental car agencies are "off" the airport so you will take a shuttle from the car rental lot to the airport.