This paper proposes low-overhead and low-complexity channel estimation (CE) of frequency-domain equalization aided faster-than-Nyquist (FTN) signaling. In the proposed CE scheme, the concept of pilot superimposition is employed, where the FTN block is designed to superimpose pilot symbols with information symbols, and thus, no dedicated time and frequency resources nor guard bands are required, resulting in a 50% reduction of the overhead. Furthermore, interference induced by the pilot superimposition is eliminated by invoking a novel scheme, referred to as spectral interference alignment, where a data-dependent sequence is subtracted from transmitted information symbols. The theoretical mean-square error (MSE) of the proposed CE is derived, which verifies that the MSE is no longer affected by interference due to the pilot superimposition.