After almost two years without scoring, he scored against Siena on 2 December 2012, giving Roma a 1–2 lead away. Roma eventually won the game 1–3, with a brace from Mattia Destro. He scored again on 3 March 2013, also in a 3–1 win, against Genoa at the Stadio Olimpico. He was substituted on for striker Pablo Osvaldo in the 81st minute and eight minutes later, in the 89th minute, he scored a goal that sealed the match. After the appointment of Aurelio Andreazzoli as caretaking manager, he received significantly more playing time than under the Czech Zdeněk Zeman. He finished the season with 16 league appearances, only four as a starter, with two goals scored; under manager Aurelio Andreazzoli, he was left on the bench in Roma's 1–0 Coppa Italia Final defeat to cross-city rivals Lazio. On 29 June 2013, Perrotta announced his retirement from professional football.