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."