Late goals in each half from Mitch Hand and George Gaskin gave the Marigolds victory in a game that had to be delayed for 20 minutes due to floodlight failure before kick-off.
Whittington, whose side travel to Sevenoaks in the FA Vase on Saturday, said: “Obviously, the result was disappointing, but I can’t complain too much about the performance. We worked hard and deserved to get more than we did from the game.
“We had four players out injured and unavailable so I had to call up a number of reserve players to the squad and I’m pleased with how they stepped up.
“There are a lot of positives to take from the game and now we need to build on them and try to bounce back on Saturday.”