Societies are complex systems which tend to polarize into sub-groups of individuals with dramatically opposite perspectives. This phenomenon is reflected -- and often amplified -- in online social networks where, however, humans are no more the only players, and co-exist alongside with social bots, i.e., software-controlled accounts. Analyzing large-scale social data collected during the Catalan referendum for independence on October 1, 2017, consisting of nearly 4 millions Twitter posts generated by almost 1 million users, we identify the two polarized groups of Independentists and Constitutionalists and quantify the structural and emotional roles played by social bots. We show that bots act from peripheral areas of the social system to target influential humans of both groups, bombarding Independentists with violent contents, increasing their exposure to negative and inflammatory narratives and exacerbating social conflict online. Our findings stress the importance of developing countermeasures to unmask these forms of automated social manipulation.