Peyton Peyton passed for 307 yards, hooking up with Wes Welker and Julius Thomas on scoring strikes for the Broncos (2-0).
The elder Manning -- coming off a seven-touchdown performance last week against Baltimore -- had prevailed over Eli twice previously, both times when he was playing for the Indianapolis Colts.
Knowshon Moreno rushed for two touchdowns and Trindon Holliday returned a punt 81 yards for a score for Denver.
Eli Manning went 28-of-49 through the air for 362 yards and a touchdown but was intercepted four times for the Giants (0-2), who dropped a second straight to begin the season for the first time since 2007.
Victor Cruz led New York's receiving corps with eight catches for 118 yards.