The classification usually applies to the experimental conditions. Are the experimental conditions applied to an organism, or to a less than whole organism (cells culture --> all the way to test tube chemistry reactions)?
This is somewhat subjective, but in your case, since the experimental conditions are drying time of the pretty much whole organism (the tomato), I would call it an in-vivo experiment.
Think of it this way, if you treat animals with X and examine Y, this is an in-vivo experiment regardless of whether you are isolating proteins, DNA, RNA etc... to examine afterward to characterize the change in Y.
Now if you isolated cells first from mice and plated them to grow in cell-culture, and then treated with X to examine the same endpoint, this has become more ex-vivo.
In-vitro would be to isolate a single enzyme from mouse cells, put into a test tube, and examine its ability to reduce some substrate after X treatment.
In your case, if you isolated enzymes from tomatoes and then used them in a test-tube to reduce some agent and measure activity before and after a given treatment, this would be more ex-vivo and have gone all the way to in-vitro.
EDITED: Matt pointed out I had confused in-vitro and ex-vivo on my continuum and he was correct.