First-half efforts from Gareth McAuley and Kyle Lafferty handed the Green and White Army a comfortable 2-0 victory over the side ranked 151st in the world as they registered 26 shots on goal throughout the 90 minutes.
Despite their wastefulness, O'Neill told Sky Sports after the game that he was "delighted" to register his second successive win in their Group F campaign.
He said: "I am delighted with three points, especially with the performance and the intensity of our play. I knew we could not maintain the intensity through the second half, but we saw the game out.
"We have worked hard all week. The emphasis in our training was on getting that intensity, playing high up the pitch and I don't think the scoreline at half-time did us justice, given the quality of our play.
"We go now in a confident mood to Greece on Tuesday. Belief is developing in the squad all the time."
The win means that Northern Ireland are currently top of Group F and are the only side with a 100% record.