The Luton chief saw Town reduced to 10 men after just four minutes when skipper Alan Sheehan was shown red for clashing with Imps striker Matt Rhead off the ball.
They also fell behind from the ensuing free kick, only for James Collins to draw the hosts level on the half hour.
Lincoln hit back immediately to lead through Matt Green, before midfielder Harry Anderson was dismissed moments as James Justin levelled for Town in the closing stages of an action-packed first period.
Town then wrested control of the fixture in the latters stages of the second half, as goals for Danny Hylton and Harry Cornick sealed a vital victory, with Jones saying: “That’s my best win for lots of reasons.
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“The atmosphere was wonderful from start to finish, both sets of fans to be fair, they came in numbers, but our fans were just outstanding, absolutely outstanding,
“A lack of discipline from our captain, which I’ll deal with as I’m not having that at my football club, especially in big games like this, put us right on the back foot, then a goalkeeping error put us even further on the back foot.
“Then we showed what a quality side we are, because right up until they scored their second goal, we were wonderful with 10 men.
“We kept the ball, penetrated, caused them problems and looked by far the better side.
“Then we scored, then they scored from what they do, in terms of putting it in your box and they’ve got that many giants, they’re going to have second balls and things like that.
“Then we got the goal before half time which was a real momentum shift, then second half, pretty even, but it was wonderful from us today.
“The energy we showed, the structure we showed, the quality in possession, the cutting edge, everything we work on every single day and that’s what makes me so proud, that’s why I’m saying it was my best win.
“The structure, the way we played, the way we passed, the bravery, the technique, the quality that a Luton Town side showed with 10 men.
“I’m going to go home and watch that with a glass of wine and I’m going to love it, I’m going to absolutely love watching that, me and my dog are going to love it, brilliant.”