The Nigeria international was handed his third start since teaming up with the Goodison Park outfit in the summer.
Iwobi was deployed to the left-wing and delivered good performances but his effort could not help his side avoid defeat as Jeff Hendrick’s strike made the difference in the encounter.
The Toffees looked to be on the path to secure their fourth away draw of the season before Seamus Coleman was sent off in the 56th minute.
Sean Dyche’s men capitalised on their numerical advantage with Hendrick scoring the match-winning goal in the 72nd minute.
Iwobi featured for the duration of the game in his sixth appearance for the Goodison Park outfit this season.
The defeat saw Everton drop to 17th spot in the Premier League log with seven points from eight games.
The 23-year-old will be expected to lead the Super Eagles to victory when they face Brazil in an international friendly on October 13.