If simply going by wins and losses, Dak is 3-2 against Wentz (Wentz didn't play in the last game in 2017). So yes, in wins and losses he's out played Wentz.
Statistically? He really hasn't.
In the five games where both QBs played:
Wentz - 67.2% completion percentage, 1203 yards, 10 TDs, 1 interception, 100.0 rating
Prescott - 64.9% completion percentage, 1194, 6 TDs, 6 interceptions, 82.8 rating
Now, I am not suggesting you take Wentz over Prescott based on this sample of games, but the idea that Prescott has outplayed Wentz in head to head matchups isn't born out by the stats.