Full dimension (FD) MIMO, whereby a 2-dimensional (2D) antenna array is placed at the base station, has been known as a promising solution to economize spatial size of practical massive MIMO systems. To exploit such spatial resource for system performance enhancement, e.g., via three-dimensional beamforming, accurate estimation of the direction-of-arrival (DoA) of the signal sources is necessary. Existing DoA estimation methods using 2D arrays typically resorted to joint search over the 2D angular domain; however, the required algorithmic complexity would be prohibitively large, especially in the massive MIMO scenario. This paper proposes a two-stage low-complexity DoA estimation scheme, in which two MUSIC algorithms are performed for estimating, respectively, the elevation and azimuth angles of the impinging sources. Detailed flop count analyses are provided for justifying the low-complexity advantage. Various numerical simulations are also used to illustrate the performance of the proposed scheme.