The Toffees hit the ground running in the encounter after Dominic Calvert-Lewin opened the scoring with only six minutes into the tie.
Four minutes later, Iwobi played a low cross to the 22-year-old England U21 forward to poke home for his second goal in the game.
The first-half efforts were enough to secure victory for the Goodison Park outfit against the Championship side.
Iwobi has now featured in six games across all competitions for the Toffees this season, scoring two goals.
The Super Eagles star will hope to continue the brilliant form in their Premier League outing against Manchester City on Saturday.