Johnson came through the ranks at Watford and went on to become the club's youth coach in the late 1990s under Graham Taylor, and this was the first time Yeovil had faced the Hornets.
Watford dominated the match but three goals, which all came against the run of play, helped move the Glovers up to 22nd and they are now five points from safety.
The victory also made it six games without a win for Watford and four consecutive defeats at home.
Johnson said: "It was a nice homecoming. I have been here as man and boy.
"I helped build the old dog track here many years ago, during a time when I spent more time doing that than playing football. I then came back here and had some great times working for Graham Taylor."
However, he added: "I didn't come here and want to win more because it was Watford. After all it was 14 years ago since I last worked here and 20 years before that.
"But I do always look out for their results and I have a soft spot for them.
"It was more about knowing they can score goals and finding a way to stop them."
After a first half dominated by the Golden Boys, Yeovil snatched an opening goal in injury-time through a Byron Webster header.
New loan signing Ishmael Miller, one of three debutants, made it 2-0 with another header eight minutes after the restart and the salt was well and truly rubbed in the wounds during second-half injury time when Joe Edwards scored following a counter attack.
Johnson said: "It is a massive win. Watford would have been fighting for a play-off place with a win this afternoon and most of the Watford fans would have seen this as an easy three points because of our poor league position.
"But we have been unlucky this season and should have seven or eight points more than we do.
Watford boss Gianfranco Zola's mood was a polar opposite of Johnson's, as expected, but he did reiterate his belief that the players will turn the club's fortunes around.
He said: "Today was a game where we couldn't really [afford to] lose so we are certainly in a difficult moment but I believe in this group and in these players.
"I believe we can get out of it. We will have to work harder."
Zola was asked if his job was at risk considering their recent form. He replied:
"There is no point asking questions that I can't answer.
"But I don't need the threat of being fired or sacked to push me to react or do more. There is no need for that."