We study the capillary interactions between ellipsoidal Janus particles adsorbed at flat liquid-fluid interfaces. In contrast to spherical particles, Janus ellipsoids with a large aspect ratio or a small difference in the wettability of the two regions tend to tilt at equilibrium. The interface deforms around ellipsoids with tilted orientations and thus results in energetic interactions between neighboring particles. We quantify these interactions through evaluation of capillary energy variation as a function of the spacing and angle between the particles. The complex meniscus shape results in a pair interaction potential which cannot be expressed in terms of capillary quadrupoles as in homogeneous ellipsoids. Moreover, Janus ellipsoids in contact exhibit a larger capillary force at side-by-side alignment compared to the tip-to-tip configuration, while these two are of comparable magnitude for their homogeneous counterparts. We evaluate the role of particles aspect ratio and the degree of amphiphilicity on the interparticle force and the capillary torque. The energy landscapes enable prediction of micromechanics of particle chains, which has implications in predicting the interfacial rheology of such particles at fluid interfaces.