We present an investigation of the electromagnetic pion form factor, $F_pi(Q^2)$, at small values of the four-momentum transfer $Q^2$ ($lesssim 0.25$ GeV$^2$), based on the gauge configurations generated by European Twisted Mass Collaboration with $N_f = 2$ twisted-mass quarks at maximal twist including a clover term. Momentum is injected using non-periodic boundary conditions and the calculations are carried out at a fixed lattice spacing ($a simeq 0.09$ fm) and with pion masses equal to its physical value, 240 MeV and 340 MeV. Our data are successfully analyzed using Chiral Perturbation Theory at next-to-leading order in the light-quark mass. For each pion mass two different lattice volumes are used to take care of finite size effects. Our final result for the squared charge radius is $langle r^2 rangle_pi = 0.443~(29)$ fm$^2$, where the error includes several sources of systematic errors except the uncertainty related to discretization effects. The corresponding value of the SU(2) chiral low-energy constant $overline{ell}_6$ is equal to $overline{ell}_6 = 16.2 ~ (1.0)$.