Crowd favourite Defoe had hit the bar and been frustrated by Boro goalkeeper Brad Jones, and replacing him with Robbie Keane in the 69th minute prompted booing from home fans.
However, Keane had a hand in Spurs' opener three minutes later, with Tom Huddlestone sealing a 2-0 win and a place in the fourth round.
"I don't think it's about booing me because a minute later they are singing my name," said Jol.
"I am in a very good position here and that is what I deserve, I gave them a bit of success over the last couple of years - no-one could have done better.
"I'm not someone to fear things. They say in Holland 'have no fear Jolly is here'."
While this substitution had an immediate impact, Jol's decision to bring Defoe on for Keane in a Premier League match earlier in the season against Fulham led to Spurs letting a 3-1 advantage slip.
"You can leave it and wait or make a decision," Jol added. "I've had around 150 games, maybe 170, and they normally come off, maybe a couple of them didn't.
"I make brave decisions all the time because I want to win.
"Everyone will be involved, that's what I tell them. Darren Bent was on the bench."