I'd say for any particular workout, if you really feel like throwing up, it's time to back off and go home.
However, use a high level intensity at least twice a week, keep this up for a couple more weeks, and your body will just get used to it. Soon, you'll go to the gym and do your usual nauseating workout, and not feel nauseated. Just don't overdo it, give yourself a little rest in between the really heavy workouts.
Also, lemme try reading between the lines a bit here. Recently, you had shoulder surgery, which forced you to do much less upper body work. You didn't want to quit working out entirely, so you switched to doing more lower body work instead.
And now you're learning that serious lower body work is very taxing on your entire system. Could this be what's happening to you? I mean, maybe you just didn't train enough lower body in the past?