The shortlist of 10 also included an astonishing effort from the Northern Ireland Premier League and two goals from the World Cup.
Kumi Yokoyama made the list when she dribbled through five opponents before slotting into the bottom corner during Japan's semi-final against North Korea at the U17 World Cup.
The two World Cup goals selected were Siphiwe Tshabalala's thumping drive for South Africa in the opening match against Mexico and Giovanni van Bronckhorst's spectacular strike for the Holland in the semi-final against Uruguay.
Messi has produced a number of contenders in the last few months but FIFA went for his La Liga goal for Barcelona against Valencia when he wriggled through the opposing defence before slipping the ball home.
"The final list has been drawn up using the following criteria: aesthetics; the importance of the match; the absence of luck or an opposition mistake as a factor making the goal possible; fair play; and the date, with only goals scored between January 1 and October 15 counting," FIFA said.