Messi received 206 points out of a possible 210 from the panel of 21 voters, while Barcelona got 202. They are on top for a second straight week, and the third time together in five weeks.
''In a lot of weeks, Rooney would have been higher on my ballot based on his one goal from distance alone, but this was a week with a lot of great players doing great things,'' said Tom Timmermann of The St. Louis Post-Dispatch.
Madrid was ninth, while Spanish league-leading Atletico Madrid was sixth after beating Real Betis 2-0. Atletico leads Madrid on head-to-head, and Barcelona was a point behind.
Messi overtook Madrid great Alfredo Di Stefano as the leading scorer in the clasico with 21 goals, as well as becoming the first Barcelona player to score a treble at Madrid's Santiago Bernabeu.
''Barcelona was not in its best form, neither was Messi. But having Real Madrid on the other side of the pitch had a huge effect on this team, and Barcelona played its best game of the season,'' said Ubiratan Leal of trivela.com in Brazil. ''It was intense, hard fought, physically and emotionally demanding. And, in this situation, Barca seems to be always one step in front of Madrid. It was like in Guardiola's time.''
Chelsea was second after it thrashed London rival Arsenal 6-0 in Arsene Wenger's 1,000th game as manager. Two of Chelsea's scorers, Andre Schuerrle and Oscar, were ninth and 10th in the player vote.
''The winning mentality of Jose Mourinho led Chelsea to an unforgettable success against Arsenal,'' said Aurelio Capaldi of RAI Sport in Italy. ''It was an aggressive and powerful performance, capable of making Arsenal think they were just sparring partners at Stamford Bridge.''
Liverpool was third, followed by Bayern Munich, closing in on the Bundeliga title, which it could clinch late Tuesday with a win over Hertha Berlin and seven games remaining.
United enjoyed one of its better weeks as it overturned a 2-0 deficit against Olympiakos to reach the Champions League quarterfinals before beating West Ham 2-0 and polled fifth.
Robin van Persie, who scored all three goals for United in the win over Olympiakos, was seventh. He missed the West Ham game because of a serious knee ligaments injury that threatens his World Cup participation.
AP Global Soccer 10 rankings, week ending March 25
1. Lionel Messi, 206.
2. Luis Suarez, 146.
3. Yaya Toure, 98.
4. Wayne Rooney, 94.
5. Andres Iniesta, 68.
6. Angel Di Maria, 50.
7. Robin van Persie, 43.
8. Karim Benzema, 40.
9. Andre Scheuerrle, 39.
10. Oscar, 32.
1. Barcelona, 202.
2. Chelsea, 187.
3. Liverpool, 126.
4. Bayern Munich, 100.
5. Manchester United, 89.
6. Atletico Madrid, 86.
7. Manchester City, 84.
8. Juventus, 68.
9. Real Madrid, 41.
10. Paris Saint-Germain, 24.