Abstract The fidelity of splice site selection is critical for proper gene expression. In particular, proper recognition of 3′-splice site (3′SS) sequences by the spliceosome is challenging considering the low complexity of the 3′SS consensus sequence YAG. Here, we show that absence of the Prp18p splicing factor results in genome-wide activation of alternative 3′SS in S. cerevisiae, including highly unusual non-YAG sequences. Usage of these non-canonical 3′SS in the absence of Prp18p is enhanced by upstream poly(U) tracts and by their potential to interact with the first intronic nucleoside, allowing them to dock in the spliceosome active site instead of the normal 3′SS. The role of Prp18p in 3′SS fidelity is facilitated by interactions with Slu7p and Prp8p, but cannot be fulfilled by Slu7p, identifying a unique role for Prp18p in 3′SS fidelity. This fidelity function is synergized by the downstream proofreading activity of the Prp22p helicase, but is independent from another late splicing helicase, Prp43p. Our results show that spliceosomes exhibit remarkably relaxed 3′SS sequence usage in the absence of Prp18p and identify a network of spliceosomal interactions centered on Prp18p which are required to promote the fidelity of the recognition of consensus 3′SS sequences.