My grandfather developed an intolerance for high acid tomatoes. I remember him growing a large yellow 'low acid' variety. I just read an article from Dave's garden. One apparently reliable source from Texas A&M (TAMU) said that there is really no such thing as a low acid tomato. Said that any differences in acidity are negligible, and percieved difference is due to the presence of greater sugar content which causes the tomato to taste less acidic.
If I had the problem, I would experiment. Maybe do as suggested above and follow the meal with an antacid, or better yet pair the tomatoes with a balanced meal, so as to dilute or even partially neutralize the tomato acid in the stomach. Also, don't eat too much volume or too late, as that will contribute to acid reflux at night. One last note, according to the TAMU info, all tomatoes have an acidity of around 4.6. That is no where near the acidity of the stomach environment which has a pH of around 2. So there is no way that tomatoes will make your stomach contents more acidic. My guess is that some other factor is at work. Decrease the amount of tomatoes eaten at one sitting and follow the other two recs above and maybe the problem will go away.
If that doesn't work, then perhaps your body has simply developed an intolerance or an allergy to raw tomatoes. From doing a quick google, it appears that it is fairly common for a person to not be able to eat fresh tomatoes, while having no problem at all from processed tomato products. Good luck, I'm certainly sympathetic, as a loss of fresh tomatoes from my diet would be losing a best friend.
Eclectic gardening style, drawing from 45 years of interest and experience. Mostly plant in raised beds and containers primarily using intensive gardening techniques.