Winfield headed the only goal of the game at Adams Park as the Chairboys made it five consecutive victories in all competitions to stay third in League Two.
Gillingham had been riding on the crest of a wave after five consecutive victories of their own but were brought back down to earth by Waddock's side.
Waddock said: "It was tight because you had two decent sides and always felt it might only take one goal to separate us but to back up the Cheltenham result with this one is very rewarding.
"I think the fitness levels were excellent and the energy they showed in getting to the second ball and chasing lost causes just shows you what that group of players are all about.
"When they can do that, then the other side of their games comes like the way they pass the ball around. Dave (Winfield) was a colossus in defence and he got the winning goal for us, but the whole back four played very well in marshalling their front two."
Source: PA
Source: PA