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Here, we reveal its presence and underlying mechanisms in pairwise scientific collaboration by reconstructing the publication histories of 560,689 individual scientists and 1,026,196 pairs of scientists. We quantify pair synergy by extracting the non-additive effects of collaboration on scientific impact, which are not confounded by prior collaboration experience or luck. We employ a network inference methodology with the stochastic block model to investigate the mechanism of pair synergy and its connection to individual attributes. The inferred block structure, derived solely from the observed types of synergy, can anticipate an undetermined type of synergy between two scientists who have never collaborated. This suggests that synergy arises from a suitable combination of certain, yet unidentified, individual characteristics. Furthermore, the most relevant to pair synergy is research interest, although its diversity does not lead to complementarity across all disciplines. 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