The five-time champions signed off from the tournament in miserable fashion, annihilated 7-1 by Germany in their semi-final before losing 3-0 to the Netherlands to squander third place.
But Rousseff said the team could still hold its head high.
"Dear players, dear technical commission: You and Brazilian football are better than just a one-off result," Rousseff wrote in a personal letter to the team.
Brazil's loss to Germany was its greatest ever World Cup reverse and a humiliation locals are comparing with their 1950 "Maracanazo" shock loss to Uruguay.
"Without you that would never have been possible," she added. "What will remain etched on our people's hearts are the moments of joy you gave us at this Cup and which you will surely offer at Cups to come."
Rousseff responded to the Germany loss by promising government support for a thorough reform of the Brazilian game.
She wants to push reforms that might persuade young talent to apply their skills domestically rather than rush off to seek fame in Europe.
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