The home support, who were already angry at their team's showing in the first half, turned on their team's manager moments after the goal went in when Villas-Boas took off Defoe and brought on Emmanuel Adebayor to partner Clint Dempsey up front.
The Spurs fans booed the decision and chanted Defoe's name as he sauntered off the pitch before grabbing his coat and disappearing down the tunnel.
Villas-Boas explained the decision to the in-form striker afterwards, and insisted he understands the fans' angst.
"We understand that they can show their frustrations," the 35-year-old said.
"We don't do things to punish them or for the fans to show revolt. We do things for the benefit of the team.
"They want the win, but we want the win as much as them. We respect them."
Defoe has scored seven goals for club and country this season, but looked poor on this occasion.
"We spoke briefly afterwards," the Spurs boss said.
"It was obviously disappointing for him to come off since he has been on a good goal-scoring run, but the team is also important.
"We don't make the change to punish him. We make the change to improve things."