Shamir Fenelon gave the Shots the lead before Jake Gallagher doubled it in the second half, put were pegged back with essentially the final kick of the game when Andrei Jones lobbed Jake Cole in the last minute.
The Shots were good value for their victory and dominated large periods of the game, with Gallagher and Kundai Benyu having another solid game in the middle of the pitch and will be disappointed to have conceded in the final minute.
Waddock's men now have the weekend off and won't play again until Gateshead on January 21, but Waddock was pleased with how his side got their third win on the bounce.
He said: "I'm really pleased, it's a shame we didn't get a clean sheet, I think we switched off right at the end but all in all it was very good.
"The score at the end gives us momentum but I thought we played very well, had a lot of chances and the only negative was to concede at the end but all in all I'm very pleased.
"It's interesting because I can't remember Cole making a save, we done well defensively and thought the early part of the first half, our final pass once we spun off of them needed to be better but we're nitpicking after a fine performance.
"From their side, they moved the ball around well at times, had some possession but I thought we closed them down and spun off them really well during periods of that game.
"I think we had a spell about 20 odd minutes to half time where we had them right on the back foot and caused a lot of pressure, and we deserved to go in winning at half time.
"I'm pleased for Shamir, he's gone up front and caused teams problems with his pace and he's chipped in with a goal today which is pleasing."