We present a general procedure to construct 6-dimensional manifolds with SU(3)-structure from SU(2)-structure 5-manifolds. We thereby obtain half-flat cylinders and sine-cones over 5-manifolds with Sasaki-Einstein SU(2)-structure. They are nearly Kähler in the special case of sine-cones over Sasaki-Einstein 5-manifolds. Both half-flat and nearly Kähler 6-manifolds are prominent in flux compactifications of string theory. Subsequently, we investigate instanton equations for connections on vector bundles over these half-flat manifolds. A suitable ansatz for gauge fields on these 6-manifolds reduces the instanton equation to a set of matrix equations. We finally present some of its solutions and discuss the instanton configurations obtained this way.