Using a single trapped ion, we have experimentally demonstrated state-independent violation of a recent version of the Kochen-Specker inequality in a three-level system (qutrit) that is intrinsically indivisible. Three ground states of the (171)Yb(+) ion representing a qutrit are manipulated with high fidelity through microwaves and detected with high efficiency through a two-step quantum jump technique. Qutrits constitute the most fundamental system to show quantum contextuality and our experiment represents the first one that closes the detection efficiency loophole for experimental tests of quantum contextuality in such a system.