Rees completed 21-of-34 passes in the come-from-behind victory, including nine to Daniels, who finished with 177 yards.
The second of the pair's two fourth-quarter touchdowns came on an 82-yard scoring strike and handed the Fighting Irish (2-1) their first lead at 24-17.
Bennett Jackson then returned an interception 34 yards for a touchdown and the Irish went on to beat their in-state rival for a sixth consecutive time.
Rob Henry went 25-of-40 through the air for 256 yards, three scores and a costly interception for Purdue (1-2).
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