Barcelona star Messi saw his monopoly on the Ballon d'Or end on Tuesday, as Real Madrid forward Ronaldo was handed the prize at a ceremony in Zurich.
Messi, 26, held the mantle of the world's leading player for four years in a row, as he won the now-defunct FIFA World Player of the Year trophy in 2009 before reeling off three straight Ballons d'Or after the governing body merged its award with France Football in 2010.
The Argentina captain suffered an injury-hit 2013, though, and had to settle for second place on the podium this time around after being usurped by Ronaldo, who scored 69 goals for Real and Portugal last year.
However, while recognising Ronaldo's incredible form, Barca coach Martino still feels Messi should be recognised as the superior player.
"(We) congratulate Cristiano Ronaldo, the Ballon d'Or is the recognition of a year," he said.
"(But) one thing is a player rewarded for one year, and (another) is being the best in the world - and we have got the best here."
Messi made his return from a two-month lay-off with a hamstring problem in last week's 4-0 Copa del Rey win over Getafe, as he came off the bench to score a late brace.
And Argentine coach Martino confirmed that his compatriot has "completely recovered" from the injury and could return to the starting XI in the second leg of their tie on Thursday.
Martino also revealed that Neymar is fully fit after a bout of flu, but he has opted to rest the likes of Andres Iniesta, Sergio Busquets and Jordi Alba for the trip to Coliseum Alfonso Perez.
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