Nigerian striker Innocent Emeghara put the visitors ahead at Renato Dall'Ara with a 33rd-minute effort only for Panagiotis Kone to level matters five mintues before the break.
Bologna had virtually all of the remaining chances but were unable to find a winner, handing second-bottom Siena a point in their battle against the drop.
Siena might have conceded as early as the second minute when Alberto Gilardino got a foot on Saphir Taider's pass only to miss by a fraction.
Gilardino had another opportunity in the 23rd minute, springing the offside trap before being denied by the body of goalkeeper Gianluca Pegolo.
Siena scored against the run of play 10 minutes later, Alessio Sestu crossing from the left and finding Emeghara, who headed home from close range.
Bologna put things right after 40 minutes, Alessandro Diamanti's free-kick evading all the Siena defenders before being touched over the line by Kone.
The second half was a backs-to-the wall operation for Siena, starting when Diamanti and Manolo Gabbiadini combined well before the latter shot wide.
Substitute Gabbiadini had a second shooting chance after the hour mark but this time his effort was too high.
From there on it was all about Diamanti as he looked for the winner.
First he skimmed the outside of the post following a strong run and then went within inches of burying a free-kick with 20 minutes remaining.
Diamanti's final chance was less close, a left-footed attempt that failed to trouble Pegolo, as Siena held out.