Leal received the Grand Cross of the Royal and Distinguished Spanish Order of Charles III at a formal ceremony at the former Palace of the Spanish Governors.
The royal couple also presented Leal, a key figure behind Havana's restoration of colonial-era monuments, with a hand-woven banner bearing the shield of Havana.
Prior to the ceremony, King Felipe VI and his wife Queen Letizia toured Havana's historic downtown area accompanied by Leal and head of the Cuban parliament, Esteban Lazo.
The royal couple arrived in Cuba on Monday in the first official visit to the island by a Spanish king, and met the next day with Cuban President Miguel Diaz-Canel.
The official visit coincides with the 500th anniversary of the founding of Havana, and will conclude on Thursday in the eastern city of Santiago de Cuba.