- First of all the probability density for a system in a canonical ensemble to be at a given energy (i.e. with respect to a measure $dE$) is not the formula you gave but rather:
$$\rho(E) = \frac{\Omega(E)e^{-\beta E}}{\int_0^{+\infty}dE\:\Omega(E)e^{-\beta E}} = \frac{e^{S(E)/k_B}e^{-\beta E}}{Q}=\frac{e^{-\beta F(E)}}{Q}$$
we thus see that weiht associated to a given energy state is more related to a free energy $F(E)=E-TS(E)$ than the simply the actual energy.
Now, the probability density to be in a given microstate $\mu$ (with respect to some phase space measure $d\mu$) for a system in a contact with a thermostat is:
$$f(\mu) = \frac{e^{-\beta E(\mu)}}{\int d\mu\:e^{-\beta E(\mu)}}$$
- Secondly, I will try to summarize a bit what has been said by the others but in a general situation working with probabilities nstead of probability densities (there is no big difference).
It is important to realize that when a system is in contact with a thermostat at temperature $T$, you in fact have a small system, say $1$, that interacts with a big one, say $2$. The whole thing can be considered as an isolated system of energy $E$. In thermodynamic equilibrium all microstates of the isolated system are equi-probable and have a probability:
$$p(\mu) \equiv \frac{1}{\sum_{E_1}\Omega_1(E_1)\Omega_2(E-E_1)} \tag{1}$$
Here it is assumed that $E=E_1+E_2$. This is only true if there is no volume interaction between the system $1$ and the system $2$.
Now, the probability for the system $1$ to be in some microstate $\mu_1$ with energy $E_1(\mu_1)$ is nothing but the sum of $(1)$ over all the possible microstates of the system $2$ that ensure that $E_1+E_2=E$ i.e.:
$$p_1(\mu_1) \equiv \frac{\Omega_2(E-E_1(\mu_1))}{\sum_{E_1}\Omega_1(E_1)\Omega_2(E-E_1)} \tag{2}$$
What we see already is that the degeneracy of a microstate of system $1$ is the total number of microstates of system $2$ compatible with the constraint $E=E_1+E_2$.
We thus already see that the bigger $E_1(\mu_1)$, the smaller the weight associated to the microstate $\mu_1$ (if we assume that the number of microstate is an increasing function of the energy).
This general result can be made quantitative in the case of small $E_1$ and it gives the Boltzmann weight:
$$p_1(\mu_1) \equiv \frac{e^{-\beta_2 E_1(\mu_1)}}{\sum_{E_1}\Omega_1(E_1)e^{-\beta_2 E_1}} \tag{3}$$
where $\beta_2 = 1/k_B T_2$ tells us how the degeneracy $\Omega_2(E-E_1(\mu_1))$ decreases with $E_1$ for small $E_1$.