The Bees player/manager claimed his first goal for the club in the 84th minute, though winger Dani Lopez argued it was he who got the final touch.
Jake Hyde's 10th goal of the season in the 33rd minute had put Barnet ahead to keep the hosts outside of the League Two relegation zone.
Hyde netted a brilliantly-timed header from a fine inswinging Mark Byrne free-kick, with Barnet's killer second coming as Davids burst into the box on the left-hand side and steered a shot past Paul Smith, Lopez making sure it had crossed the line.
Southend had started the brighter, Britt Assombalonga twice off target with shots from inside the box during the opening exchanges.
After the break Southend huffed and puffed, with Barry Corr's drive well blocked by Dale Stephens and strong claims for a penalty after Stephens' handball, only for Davids to settle matters against Paul Sturrock's Shrimpers.