I think that you are confusing instantenous sport rate $r(t)$ with continously compounded spot interest rate $R(t,T)$.
The instantenous sport rate $r(t)$ is just a rate over infinitesimal interval $dt$ and this rate is not observable, because the shortest rate traded is overnight rate i.e. 1 day rate.
The continuously-compounded spot interest rate $R(t,T)$ prevailing at time t for the maturity T is the constant rate at which an investment
of $P(t, T)$ units of currency at time t accrues continuously to yield a unit
amount of currency at maturity $T$ i.e. $P(T,T)=1$, in formulas:
$$R(t,T)=-\frac{lnP(t,T)}{T-t}$$
then of course
$$P(t,T)=e^{-R(t,T)(T-t)}$$
where $P(t,T)$ is zero-coupon bond or discount factor.
Notice that our yield curve is not continuous but a discrete construct. Typically it is built off of instruments with maturity 1D, 2D, 1W, 1M, 3M, 6M, 1Y, 2Y, ... etc. Therefore we say that $R(t,T)$ is observable. Even if we want to trade maturity that is not on our yield curve, let's say 3.5 months, then we can do it in practice, if we pay slight premium. But we can't trade $r(t)$, we can't trade loans/depos over 1 milisecond or a few seconds interval - it is not quoted hence not observable.
Notice that if you know parameters to Vasicek model (or any short rate model) and the instantenous rate $r(t)$ then you can calculate bond prices $P(t,T)$ for all $T$ and then calculate spot rates $R(t,T)$ for all maturities $T$. Therefore the pricing equation for bonds allows you to calculate $R(t,T)$ based on $r(t)$.
Notice that
$$P(t,T)=E^Q[e^{-\int_t^T r(s) ds}]$$
then
$$R(t,T)=-\frac{ln(E^Q[e^{-\int_t^T r(s) ds}])}{T-t}$$
Ok, so how do we estimate $r(t)$?
Then we can ask, how we can use the pricing equation for bond when we don't know $r(t)$? In practice we just assume that the $r(t)$ is equal to the shortest rate $R(t,T)$ on the yield curve, 1 day or 1 week rate.
i.e.
$$r(t)=R(t,t+1/365)$$
Why? Because we can interpolate rate $r(t)$ from the yield curve. Notice that we know $P(t,t)$ - it is just equal to 1, also we know $P(t,t+1/365)$, based on these two discount factors we can interpolate $r(t)$ and it will be equal to $R(t,t+1/365)$ when we use log-linear interpolation. Please check my answer here link