Innocent Emeghara struck in the 86th minute after Pescara had come back from 2-0 down to go 17th on 30 points, three ahead of Genoa and Palermo who have a game in hand and nine ahead of the basement side.
Vincenzo Montella's Fiorentina came through a tight and largely uneventful match with Atalanta with an important win thanks to a penalty on the hour from David Pizarro after a Guigliemo Standardo handball and a fine strike from Marcello Larrondo 11 minutes later.
Fiorentina are three points behind AC Milan having played a game more.
"Like we said before the match we need to keep looking forward, but also look over our shoulders," said Montella, whose side have Lazio in their rear view mirror.
"Today gave us another push in the right direction. Our number one objective is to qualify for Europe."
Atalanta, who are 13th on 37 points and not yet safe from relegation, had German Denis sent off in the final minute for a late lunge on Fiorentina midfielder Pizarro.
All four sides were playing on the anniversary weekend of the death of Bergamo-raised Piermario Morosini, who died at the age of 25 after collapsing on the pitch while playing for Livorno at Pescara in Serie B last season.
Pescara also paid tribute to the midfielder, naming one of the stands at the Stadio Adriatico after him.
Fiorentina remain fourth but are now on 55 points, three behind Milan, who take on second-placed Napoli at the San Siro on Sunday (1845 GMT), and four ahead of Lazio in fifth.
Siena, who started the season with a six-point deduction for their involvement in match-fixing and illegal betting while in the second division three years ago, thought they had bagged the three points in the first half with an Angelo header after 14 minutes and a comical Damiano Zanon own goal 19 minutes later.
However Pescara came roaring back in an exciting second half and levelled the scores thanks to a smart strike from substitute Mervan Celik after 52 minutes and a superb Romulo Togni free-kick seven minutes later.
Both sides hit the post in a hugely entertaining second half but it was Siena who controversially won the game thanks to Emeghara.
The striker tapped home the close-range winner at the end of a a blistering counter-attack after receiving a pass from Salvador Agra, who was clearly offside when put through, enraging Pescara president Daniele Sebastiani.
"When the game was set to be all square, there was an offside goal. Once again we find ourselves having to comment on a match that was decided by others," he said.
"There have been many refereeing decisions against us in the last eight rounds. If they had given us what we were due, we'd be on 30 points right now."