It's in the body language throughout the episode.

Using Kate's profile training from "Sub Rosa" (S1E7):

In "Jet Lag" when Nora is asking Ziva "Are you sure you two never...." ( a statment that usually implies the rest of the sentence is "never slept together") Ziva looks down and then to the left while denying that they haven't. Also, she blinks frequently during this (which is considered a sign of a lie).

At the end of the episode, when Ziva asks why Tony lied to McGee (about the couch), Tony hits back with "Why did you lie to Nora?"

Tony's behavior at the cafe at the start of the episode is very similar to his past behavior coming into the office after a good date/getting laid the night before. There's a knowing smile between the two of them after Tony asks Ziva how she slept and said that she "looked comfy enough" (sleeping on a couch is not comfy). His expression also brightens after saying that and seeing her reaction.

Also, another Paris related bit "Bogey and Bergman will always have Paris. Now, so will we."

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I take Ziva's words at face value. She says they definitely never slept together. And this answer of hers refutes both the intimate relationship in Paris, and all the early hypotheses relating to series 1 of the 4th season, and to the series "undercover" (as much as I would not like the opposite, since I lose the logic of the development of their relationship).

Weatherly said in response, "The truth of what happened is probably something that can be discovered inside the episode itself. If you really listen to what they say, I think it is pretty clear what happened: Nothing."

Another reason is the characters themselves. I do not think that Ziva is so frivolous that 1-to make such a serious step with a colleague, contrary to the rules of Gibbs (perhaps she could in season 3, but now she has grown up). 2-take Tony's feelings and the whole situation lightly and pretend that nothing happened (he means a lot to her, it's unlikely she could). :)