Villarreal winger Nicolas Pepe, formerly of Arsenal, scored the only goal after just 12 minutes as the Elephants edged the Scots.
Scotland were caught out by a rapid Ivorian counter-attack, with Pepe reacting quickest to tap in after Elye Wahi’s strike hit the post.
"We get caught on the counter for the goal, which can't really happen," said Scotland captain Andy Robertson post-match.
"We want to win these games, but we're also trying out stuff. It's up to us now to go back to our clubs and be really excited for the summer."
The Scots showed flickers throughout the game, edging the stats in shots on target, but were undone by a lack of cutting edge in the final third.
Scott McTominay forced a save from Alban Lafont as they searched for a response, while George Hirst came closest after the break with a near-post header.
Ivory Coast, who thrashed South Korea 4-0 at the weekend, were content to defend their lead for much of the second half, though Amad Diallo tested Scott Bain late on and Simon Adingra struck the post during a late flurry.
The result follows Scotland’s 1-0 defeat to Japan on Saturday and raises concerns over their attacking output ahead of their first World Cup in 28 years.
Clarke's men are next up against Curacao in their final warm-up match on 30 May, before facing Haiti, Morocco and Brazil in America.