Without a win from their 10 league matches to date, and on a wretched run of five successive defeats, bookmakers were offering odds of 28-1 on a Almeria triumph.
But despite conceding a penalty to Jonas just after the half hour, Francisco Javier Rodriguez's side produced a second-half fightback with goals from Marco Torsiglieri and Aleix Vidal.
The loss was Valencia's third in a row in the league and is likely to place Serbian coach Miroslav Djukic under considerable pressure.
This latest embarrassment comes after a 4-1 humbling at local rivals Villarreal on Sunday, one Djukic claimed had led to a loss of morale amongst his players.
In front of their own fans at the Mestalla, Valencia struggled in the opening exchanges, barely conjuring a chance of note before Brazilian midfielder Jonas netted his fifth of the season from the spot after Hernan Pellarano had handled in the area.
Two fine saves from Esteban Suarez either side of the break to deny Juan Bernat and Javi Fuego kept Almeria in the hunt until the hour mark when they hauled themselves level.
On loan from Metalist Kharkiv, Argentine defender Torsiglieri rose to meet an inswinging corner from Suso to plant home a header from six yards.
Less than nine minutes later Vidal struck from 12 yards for his second goal of the season to put the visitors in front.
Helder Postiga then had two late chances to salvage a draw, but neither was able to spare Valencia's blushes.