Lafferty stole the show at Stadio Georgios Karaiskakis, grabbing a goal as O'Neill's men continued a stunning start to their Euro 2016 Group F qualifying campaign.
His strike added to Jamie Ward's opener to help Northern Ireland follow up victories over Hungary and the Faroe Islands.
They now have a haul of nine points from three games, which is their best start to a qualifying campaign for a major tournament.
O'Neill told Sky Sports: "I am obviously delighted. [Making our best start to a qualifying campaign] is a nice thing to have as a statistic but the main thing was the performance and three points.
"Every player was magnificent. 'Laff' has been fantastic in all three games. He has all the attributes and is bringing it all together.
"The second goal - the quality of his run, touch and finish - was phenomenal. What he brings is huge."
Skipper Steven Davis was equally effusive in his praise of Lafferty, adding: "We knew they were going to have a lot of possession and we had to be disciplined. We defended really well.
"I thought Kyle was the standout player. He made the difference and took his goal really well."
