In general, the halacha is that you only make a bracha achrona if you eat a k’zayis.
However, there is an opinion that you make a bracha achrona whenever you eat a complete fruit even if it’s less than a k’zayis. But it’s a macholokes and there is no clear psak. Therefore, it’s a safeik.
Since it’s a safeik, the rule is “safeik brachos l’hakel” so if you did this, I think you are not supposed to make a bracha achrona.
But I think the halacha is that you are supposed to try to avoid the safeik in the first place. In general, we are supposed to avoid safeiks if possible.
In this case, this can be done in one of two ways:
1. Eat more cherry tomatoes.
2. Eat or drink something else requiring a borei nefashos.
If I have a chance, I will try to look up and bring the sources.