A semiconductor device has a substrate and plurality of first semiconductor die having conductive vias formed through the first semiconductor die mounted with an active surface oriented toward the substrate. An interconnect structure, such as bumps or conductive pillars, is formed over the substrate between the first semiconductor die. A second semiconductor die is mounted to the first semiconductor die. The second semiconductor die is electrically connected through the interconnect structure to the substrate and through the conductive vias to the first semiconductor die. An underfill material is deposited between the first semiconductor die and substrate. Discrete electronic components can be mounted to the substrate. A heat spreader or shielding layer is mounted over the first and second semiconductor die and substrate. Alternatively, an encapsulant is formed over the die and substrate and conductive vias or bumps are formed in the encapsulant electrically connected to the first die.