Combining the ability to prepare high-quality, intrinsic Bi$_2$Te$_3$ topological insulator thin films of low carrier density with in-situ protective capping, we demonstrate a pronounced, gate-tunable change in transport properties of Bi$_2$Te$_3$ thin films. Using a back-gate, the carrier density is tuned by a factor of $sim 7$ in Al$_2$O$_3$ capped Bi$_2$Te$_3$ sample and by a factor of $sim 2$ in Te capped Bi$_2$Te$_3$ films. We achieve full depletion of bulk carriers, which allows us to access the topological transport regime dominated by surface state conduction. When the Fermi level is placed in the bulk band gap, we observe the presence of two coherent conduction channels associated with the two decoupled surfaces. Our magnetotransport results show that the combination of capping layers and electrostatic tuning of the Fermi level provide a technological platform to investigate the topological properties of surface states in transport experiments and pave the way towards the implementation of a variety of topological quantum devices.