Define authentic? Don't forget, authentic doesn't necessarily mean high quality. I might say La Puerta or the Blind Burro as far as taste goes. Maybe ¡Salud! down farther south. But if you want the whole dining experience to be "authentic", I'm not sure any of the establishments in 'Diego qualify. Most of them are, as pointed out, tourist oriented trying to push the "hip" vibe to attract regulars as the place to be. For that matter, I could even say Puesto's if you just want tacos and drinks.
Another suggestion might be, if you're staying downtown, is wait to do your south of the border dining while on the cruise (Cabo, Ensenada?) and do your night before dining at Little Italy? Just a thought for variety.
But just having an afternoon doesn't give you much time to do anything. You could do the Midway if you didn't want to do Balboa Park. Watch the Sunset at Ocean Beach? Ride bikes on the Front Walk at Mission Beach (Tacos el Trompo there)?