Luca Ceccarelli's dismissal proved the turning point as Serie A strugglers Cesena were deprived of a much-needed result at the Stadio Dino Manuzzi.
The defender was sent off in the 74th minute after bringing down Emanuele Calaio in the penalty area as he ran clear on goal.
The hosts had dominated up to that point but Franco Brienza followed up Claudio Terzi's missed spot-kick to score and then set up Erjon Bogdani to make it 2-0.
Siena flew out of the blocks but both Roberto Vitiello's free-kick and Calaio's header were off target.
Cesena's Mario Santana failed to unduly trouble visiting keeper Gianluca Pegolo and fellow midfielder Raphael Martinho shot well wide.
Francesco Antonioli saved from Brienza but Cesena took control as half-time approached, although Martinho was again wayward before Simone Del Nero went much closer.
Tommaso Arrigoni forced a good save from Pegolo and Martinho began to find his range, shooting just wide in stoppage time and again a minute after the resumption.
Pegolo fielded Dominique Malonga's effort and Vincenzo Renella curled a free-kick inches wide as the pressure grew on Siena.
But a 74th-minute breakaway saw Calaio's run halted illegally by last man Ceccarelli, bringing about a red card and a penalty.
Terzi's effort was tipped onto the post by Antonioli but Brienza was alert to the rebound and broke the deadlock.
The second goal came in the 81st minute when Brienza crossed for Bogdani to head into the top right corner.
Del Nero's wayward long-range effort was the only response from the deflated hosts, who remain bottom of the table while their fortunate opponents move seven points clear of the relegation zone.
