The answer is no.
The fact that you can bend without stretching a piece of paper should convince you of that. Consider for instance a piece of a plane and piece of a cylinder.
The question you ask can be rephrased in the following way: take a 2 dimensional Riemannian manifold $(M^2,g)$. Under which condition is there a unique isometric embedding $f:M^2\to\mathbb{R}^3$ which is unique up to rigid motion ?
The only case where I know this is true is the case of convex surfaces: assume $M$ is diffeomorphic to $\mathbb{S}^2$ and has nonnegative Gauss curvature. Then Cohn-Vossen has proved that there exist a unique convex body $K\subset \mathbb{R}^3$ (up to rigid motion) such that $(M^2,g)$ is isometric to the boundary of $K$ with the induced Riemannian metric. This shows that, on a theoretical level the intrinsic metric on $M^2$ determines the distance of between two point in the extrinsic distance given by the embedding.
However, from what I know of the proof building the embedding from the metric is not easy at all and won't give any practical way to compute the extrinsic distance between two points in terms of the intrinsic geometry of the surface.
EDIT: I'll come back later to add some references.