There may be lots of train options, but to get from Paris to Saint-Emilion, I'm guessing you'd have to actually do some kind of train or bus transfer change(s) or tranfer(s) to actually take public transport from Saint-Emilion to Paris. If you're already driving from Spain, maybe you'd be keeping your rental car to get to Saint-Emilion, than could drop it off in Bordeaux, and take the train from there to Paris. Maybe, though, you're planning on picking up a car in France, avoiding possible expenses of dropping a car off in a different country than the one where you picked it up, if you're driving in Spain too.
Anyway, for what it's worth, years ago, in the days of francs not euros, we did the trip in reverse, starting in Paris, and taking the train, but actually breaking the trip up into 2 days, and staying in Amboise, in the Loire Valley, the first night. After renting bikes and pedaling out and back to visit the Chenonceau chateau, we caught the train to Bordeaux, where we picked up our rental car for the drive to our gite outsde Saint-Emilion. Can't tell you the price, but we saw lots of countryside over our two legs of the journey. We then drove around wine country for a few more days days, seeing a lot but taking a slower pace.
Nowadays, as Adam mentioned, a direct train from Bordeaux to Paris could be cheaper and faster than you were originally indicating, if time was of the essence and you weren't tied to having a car. However, if you have the extra time and didn't mind backroads, and have an extra day to spare, taking a car would get you off the Autoroute, let you experience the countryside via byways, and taking 2 days to do it could cut the overall driving time each day. Either way, being in southwestern France means you can't make a truly bad decision. Is time or money a bigger concern? Or scenery? .