In many futuristic communication systems, integrated sensing and communication (ISAC) is emerging as a crucial use case, with wide applicability in vehicle-to-everything (V2X) scenarios. As orthogonal time frequency space (OTFS) is being investigated as a possible waveform for high-velocity scenarios, in this work we address the challenging fractional delay-Doppler (DD) bin shifts estimation by considering an OTFS-based multistatic ISAC system. We make the problem pilot agnostic and propose a novel two-dimensional delay-Doppler (2D-DD) virtual array incorporating the bin shifts as phase information. To jointly estimate the fractional DD bin shifts, two algorithms, DD-OMP and DD-ESPRIT, are proposed using such a 2D-DD virtual array, based on orthogonal matching pursuit (OMP) algorithm and estimation of signal parameters using rota-tional invariance (ESPRIT), respectively. The proposed algorithms are further analyzed to determine: a) maximum number of targets that can be identified using DD-OMP and DD-ESPRIT; b) Cramer-Rao lower bound (CRLB); and c) computational complexity. Simulation results underscore the effectiveness of the proposed algorithms to achieve improved target parameter estimation and communication link performance. Being super-resolution schemes, this improvement in performance is reflected even at lower bandwidths and is independent of the pilot structure, thus making them attractive for ISAC systems.