If you're flying into SJ, consider driving the rental car north to Fu Lam Mum in Mountain View. It's always hopping till midnight due to the 'late night dim sum menu'. Not the best food, but not bad hong-kong-ish, and a decent scene of hackers and random people. You'll have a longer drive to wherever you're staying, but...
That place doesn't have much in the way of cocktails. They claim to make cocktails and have a little bar, but I've never ever seen anyone order one.
Another option, further out of your way, is Renzo in Palo Alto, a recent addition. Bar's open until two but they're claiming kitchen till midnight. Decent sitdown and unwind. There's a few other kitchens open till midnight in PA, but I think that's the one you're looking for.
Santana Row, I don't see anything open after 11pm. Left bank, which does somewhat meet your parameters even if the food is average, closes at 11pm.
If you really want downtown, it's really all about original joe's. Remember, San Francisco isn't a great late night town, and San Jose.... well, you're getting the picture.
Your question about Union Square is asked constantly. For that request, if you don't like last week's answers, start a new topic.
Nothing in Japantown is open past 10 (Except that bar on Taylor St.)
If you're cool with soju or Hite for drinks, there are a few Korean restaurants in El Camino Real in Santa Clara that are open at that time. Tobang and #1 Restaurant are both open until midnight. Jang Mo Jip, Seoul Halmae Bossam (on San Carlos) and Rumors (which is more a bar, but they do have a full food menu) are open until 2 AM.
Most of the better food establishments will not be seating guests that late, but Santana Row may have a few options - Cazuelas, Straits, Left Bank should still be open...Rosie McCann's for sure... all have acceptable food.
Where in San Jose will be you be prior to 11 PM?
355 Santana Row, San Jose, CA 95128
11pm Dinner/Drinks? If you're in downtown San jose I'd recommend going to Single Barrel for some cool cocktails then going to good ole la vic's for a burritto and yummy orange sauce. There's not much for fine dining at that late hour...
Sitdown... there's Chinese Places that are open late night but the most you're going to get for drinks is Heineken and Tsing Tao's