Measurements of the proton and deuteron $F_2$ structure functions are presented. The data, taken at Jefferson Lab Hall C, span the four-momentum transfer range $0.06 < Q^2 < 2.8$ GeV$^2$, and Bjorken $x$ values from 0.009 to 0.45, thus extending the knowledge of $F_2$ to low values of $Q^2$ at low $x$. Next-to-next-to-leading order calculations using recent parton distribution functions start to deviate from the data for $Q^2<2$ GeV$^2$ at the low and high $x$-values. Down to the lowest value of $Q^2$, the structure function is in good agreement with a parameterization of $F_2$ based on data that have been taken at much higher values of $Q^2$ or much lower values of $x$, and which is constrained by data at the photon point. The ratio of the deuteron and proton structure functions at low $x$ remains well described by a logarithmic dependence on $Q^2$ at low $Q^2$.