This letter studies the pilot contamination (PC) problem for massive multiple-input multiple-output (MIMO) networks with coexisting terrestrial users and unmanned aerial vehicles (UAVs). Due to the strong line-of-sight (LoS) air-to-ground channels between UAVs and base stations (BSs), UAVs usually cause a more severe PC issue as compared to the traditional terrestrial users. To mitigate the PC caused by UAVs, we propose a low-complexity distributed scheme by exploiting the full-dimensional beamforming of massive MIMO BSs and the angle-dependent LoS channels between them and high-altitude UAVs. Numerical results show the effectiveness of the proposed pilot decontamination scheme and the significant signal-to-interference-plus-noise ratio (SINR) gains in both the uplink and downlink after pilot decontamination.