Villas-Boas’ decision to replace the England striker with Emmanuel Adebayor whilst losing 1-0 in the 57th minute was met by a chorus of boos from the Spurs faithful, who clearly favoured a more attacking approach.
But the former Chelsea manager has defended his decision, urging the players not to take such decisions personally.
"For sure it is not something that is very pleasing to see," the 35-year-old told reporters when questioned on Defoe’s actions.
"The most important thing for the players to realise is that we do things for the benefit of the team. We understand individual frustrations but we, as a team, are more important.
"The game wasn't going well for Defoe in our thought process. Maybe he could think the opposite but we don't take him off to punish him. We took him off to improve the team."
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There have been reports in some sections of the media that Adebayor has been unhappy with his lack of game time at White Hart Lane this season, but Villas-Boas has insisted that the Togolese striker has only been sidelined because of injuries.
"We're quite happy with his attitude," he continued.
"He had an injury which took him out for six games and then another injury took him out for two games. We have the injury records if you want to look at them.
"From the 11 games that we've played, I think he's been out for eight of them and he wasn't here at the start of the season.
"In the games when he was available he showed the quality striker that he is. We have no doubts whatsoever. We have him fit now and hopefully ready for the next upcoming games. We know his ability."