The Polish keeper is accused of throwing a bottle towards fans in the Chapel Stand, after Clint Dempsey scored Spurs' second goal.
Boruc, who was making his home debut for Southampton, had come in for criticism from supporters following a defensive mix-up that allowed Dempsey to stab home from close range.
In the aftermath of the alleged incident, the stopper was booed by large sections of the crowd in the Chapel Stand.
In a statement, the club said: "Southampton Football Club can confirm that it is investigating allegations of an incident involving Artur Boruc that occurred towards the end of the first half during Sunday's match against Tottenham Hotspur.
"The club takes such allegations extremely seriously and will deal with the matter in the appropriate manner.
Source Daily Echo
Source: Saints Mad