Winless Sampdoria, leading 1-0 with a 41st-minute goal from Gianluca Sansone, thought they had added a second when Nicola Pozzi tapped the ball in after Angelo Palombo's free kick was spilled by goalkeeper Daniele Padelli.
There was no hint of offside or any other infringement but referee Andrea Gervasoni ruled out the goal, causing angry protests from the home players.
"The referee told Palombo that after the free kick, that was the end of the half," Sampdoria coach Delio Rossi told RAI television.
"I don't want to criticise the referee...but at 2-0, it would have been a completely different game. In an even game, these incidents can be decisive."
The incident was reminiscent of the Brazil-Sweden game at the 1978 World Cup when, with the score 1-1, Brazil took a corner and referee Clive Thomas blew for time while the ball was in the air, seconds before it was headed it into the Swedish net.
Ciro Immobile and Alessio Cerci, from a penalty, put Torino 2-1 ahead after the break, only for the visitors to find themselves on the wrong end of an equally controversial decision in stoppage time.
Eder went down in the penalty area and, although it appeared he had crashed into a defender, the decision went the other way and the Brazilian himself fired home the penalty for a 2-2 draw.