In the 2009 Davis Cup quarterfinal tie, Russia was upset by the Israel Davis Cup team on indoor hard courts at the Nokia Arena in Tel Aviv. Russia was the top-ranked country in Davis Cup standings, and the stage was set by Safin, who prior to the tie told the press: "With all due respect, Israel was lucky to get to the quarterfinals." Safin was held out of the first day of singles, and then went on to lose the clinching doubles match in five sets partnered with doubles specialist Igor Kunitsyn.
Safin started the 2009 season by playing in the Hopman Cup event in Perth with his sister, Dinara Safina. He arrived at the event sporting a bandaged right thumb, two black eyes, a blood-filled left eye, and a cut near his right eye, all suffered in a fight several weeks earlier in Moscow. In the 2009 Hopman Cup, the pair played off in the final representing Russia, but each was defeated in the singles rubbers. Safin said he had decided to play the 2009 season because of a great offer from his manager Ion Ţiriac, he made this decision despite not having a coach.
Safin's final tournament as a professional tennis player was at the 2009 Paris Masters. In the first round, he saved three match points with three aces against Thierry Ascione, eventually prevailing with a total of 24 aces and 41 winners. On 11 November 2009, Safin's career ended with a second-round defeat by reigning US Open champion Juan Martín del Potro, after which a special presentation ceremony was held on Centre Court at Bercy. Fellow tennis players who joined him in the ceremony included Juan Martín del Potro, Novak Djokovic, Gilles Simon, Tommy Robredo, Frederico Gil, Ivo Karlović, Albert Costa, Marc Rosset, and Younes El Aynaoui.