Greece, who have qualified for next year's European Championships finals as Group F winners, had not lost since Portuguese coach Fernando Santos took the helm after the 2010 World Cup.
Victor Piturca's side, who failed to qualify for Euro 2012 after finishing behind France and Bosnia in Group D, took the lead courtesy of Gabriel Torje's powerful finish in the game played at Austria's Cashpoint Arena.
Greece captain Giorgos Karagounis equalised with a brilliantly-executed curling 34th minute free-kick before Romania put the Euro 2004 winners to the sword after half-time with goals from Cristian Tanase and Alexandru Chipciu.
Santos made eight changes from the side which drew 1-1 with Russia four days earlier, including handing a debut to 17-year-old goalkeeper Stefanos Kapino.
But the Panathinaikos keeper had a difficult night, conceding at his near post after 17 minutes when Torje drilled home a low shot following a cross from Tanase.
Karagounis's goal, from a right-footed shot over the defensive wall after Angelos Charisteas had won a free-kick on the edge of the penalty area, proved to be the highlight for Greece.
Romania went 2-1 up through a superb dipping volley from Tanase following Marius Niculae's flick-on before substitute Chipciu prodded home a third goal nine minutes from time.
