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Gianluca Sansone threatened for the hosts early on, but saw his close-range header blocked on the line.
They were inches away from taking the lead on the stroke of half time as Daniele Gastaldello's header came back off the post.
Against the run of player the visitors were awarded a penalty in the 64th minute when Shkodran Mustafi dragged down Victor Obinna, as the striker looked to follow up his own effort that had hit the post.
Cyril Thereau stepped up and made no mistake from the spot with a confident finish into the bottom corner.
Sampdoria almost equalised immediately, but Eder drilled his low effort just wide of the far post.
With nine minutes left to play, the hosts drew level as Eder latched onto Regini's pass before firing a strike past Agazzi.
Despite their numerical disadvantage, Sampdoria pushed for a winner and found the net in the third minute of stoppage time.
Renan whipped in a low cross and Soriano pounced to drill a strike into the corner and steal the three points for his side.