The South Americans booked their place at the Maracana after producing a solid defensive performance en route to beating the Netherlands in a penalty shootout on Wednesday.
The Barcelona ace enjoyed a goal-laden group stage but has since been unable to add to his four-goal haul in the knockout rounds. However, Beckenbauer insists that Germany cannot afford to discount the "superstar".
"To overcome this defence will be a huge challenge for the Germans," the 68-year-old, who won the competition with Germany as a player and a coach, told The Hindustan Times.
"And of course, there is the superstar Lionel Messi, who, if you don't keep him under control, could decide the final with one stroke of genius."
Sunday's showpiece kicks off at 8pm.