Mooney struck first just after the hour when he was hauled back in the box by defender Shaleum Logan, and got up to fire his penalty into the bottom corner.
Batt sealed the points five minutes from the end when he raced onto a slide rule Moses Odubajo pass to coolly slot home beneath keeper Richard Lee.
Slade said: "We got in at half-time and said to each other that we could do better. After the break we stepped it up and deserved the win.
"There is a real togetherness in this squad. We are a small group and each one of them knows exactly what they need to do for each other.
"There are no energy suckers in the side. They are all energisers and they all know that our form is based around working as a team and an incredible shared will to do better."
Promotion favourites Brentford looked like a collection of individuals against the dogged east Londoners, who always looked dangerous on the break with Kevin Lisbie's pace a constant threat.
Slade admitted: "Brentford looked the better side in the first half. They have a big squad and are going for promotion, but we knew we could do better and we did."