Kari Arnason broke the deadlock before Alfred Finnbogason nodded into an empty net after Everton midfielder Gylfi Sigurdsson’s shot was parried.
Ghana struck back midway through the second period through Kasim Nuhu before Atletico Madrid midfielder Thomas Partey secured a draw on 87 minutes.
Iceland will now go into their first World Cup without a win in four games.They begin their campaign on Saturday, 16 June, against Argentina in Moscow.
Ghana failed to qualify for the World Cup for the first time since 2002.