The University of Navarra's Economics, Sport and Intangibles Research Group calculated "media value" by monitoring internet presence and the volume of press articles and gave Argentina forward Messi the top ranking for players of 21.6 points.
Real's record signing, Portuguese international Cristiano Ronaldo, was second with 19.6 and Manchester United's England striker Wayne Rooney third with 13.6.
European and world champions Barca topped the clubs' ranking with 96.6 points thanks to their haul of six trophies in 2009, with Real jumping to second, on 83.0, from fifth in a similar study published in June 2009.
Manchester United were third on 65.4, followed by Chelsea (59.7), AC Milan (56.2) and Liverpool (49.1).
"There has never before been a similar gain in media value in such a short time in the five seasons we have been conducting this study," author Francesc Pujol said of Real's climb up the club ranking.
Real president Florentino Perez spent around 250 million euros on players in the close season, including a record 94 million euros on Ronaldo, 67 million on Brazilian playmaker Kaka and 35 million each on striker Karim Benzema and midfielder Xabi Alonso.
Pujol, a professor of economics, said the club's higher media value suggested they would be able to earn more from commercial activities such as marketing and merchandise that would help offset the huge outlay on players and wages.
However, he warned that the initial boost would only be maintained if Real were successful in Europe's top club competition, the Champions League, in coming seasons.
Real had taken over from Barca and Manchester United in some key markets, especially in South America, where the English club was no longer the leader in any country, the study showed.
The sale of Ronaldo to Real had contributed to United losing their position of dominance in 13 out of 21 countries in which they were previously number one, including the United States, China, Brazil and Portugal.
