He was well clear of the rest of the field and pulled off his vest as he came around the final bend, put it in his mouth and waved to the crowd.
Mekhissi-Benabbad then held it in his hand as he sprinted down the final straight for what appeared to be his third successive European gold in the event but turned out to be a premature celebration.
He initially received a yellow card from a track official for "acting in an unsporting or improper manner" before starting his lap of honour.
But he was later disqualified after Spain, whose athletes finished fourth and fifth, made an official protest citing rules on around clothing.
Mekhissi-Benabbad's compatriot Yoann Kowal, who had moved from fourth to second in the final 200 metres, took gold instead, ahead of Krystian Zalewski of Poland and Spain's Angel Mullera.
Mekhissi-Benabbad has been involved in controversy in the past and was once suspended along with team mate Mehdi Baala after they traded blows following the 1,500 metres at a Diamond League meeting in Monaco.