The Argentina defender's previous deal was due to expire this summer and there were doubts as to whether Samuel would stay at the Nerazzurri after he made just 16 Serie A appearances in an injury-hit season last term.
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"I'm very happy to have renewed my contract for another year," the centre-back told the club's official website.
"Along with my team-mates, I hope I can give Inter a positive year and repay the club for the faith they've shown, since they still believe in me."
Samuel's contract extension comes only days after club icon Javier Zanetti signed a new deal until 2014.