Marco di Vaio had put the hosts in front in the fifth minute at the Stadio Renato Dall' Ara but Santana saved his team from defeat by grabbing the equaliser midway through the second half.
The result did little to improve either team's plight, with both still too close to the relegation zone for comfort.
The game could hardly have got off to a better start for Bologna, with Di Vaio heading Federico Casarini's right-wing cross into the top corner following the first attack of the game.
Bologna almost doubled their advantage on the counter-attack just after the half-hour when Vangelis Moras set up Francesco Della Rocca, but he could not find the target from 15 yards.
The hosts were indebted to their goalkeeper for preserving their half-time advantage, though, Emiliano Viviano pulling off a fine diving save to deny Lorenzo de Silvestri two minutes before the break.
The Viola had another chance to restore parity two minutes after the interval when Khouma Babacar turned on the edge of the box, but he lashed narrowly wide of the near post.
Twenty minutes later, though, they had their equaliser. Babacar instigated a swift counter-attack down the right from which Alessio Cerci found Santana, who tapped home from close range.
Santana turned provider for Alberto Gilardino to clinch all three points five minutes later, but the Italy striker headed over the bar with only Viviano to beat.