The New York Giants played against the Indianapolis Colts on September 10, 2006 and the Colts won. So, Peyton did beat Eli.
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Eli and Peyton have played against each other twice and Peyton's team has won twice, making Eli Manning's record against Peyton 0-2
Not in a game their teams played against each other in, no. but eli does have two superbowl wins now and peyton has one. peyton does have 4 mvp awards tho, which is more than eli