"Today we're all happy, because we saw how two people who had been so far apart for so many years took a step closer yesterday," Francis said today in his first public comments about the breakthrough.
In remarks to a group of new ambassadors to the Holy See, Francis said diplomacy was a "noble job ... A work of small steps, of little things that always end up making peace, to bring people's hearts together and spread fraternity among peoples."
He offered the Vatican as a facilitator and an agreement was hammered out at the Vatican in October.
Francis' seasoned top diplomat, Secretary of State Cardinal Pietro Parolin, helped seal the deal.
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Parolin told Vatican Radio today that the Holy See's efforts to end the standoff had been going on for years, but that Francis' involvement was "decisive."
"The pope has said it many times and I like to repeat it: When there are problems, you need to have dialogue. And the greater the problems, the greater the need to have dialogue."
Ortega was decisive in improving ties between the Catholic Church and the officially atheist state since he became Havana archbishop in 1981.
He oversaw the visits of two popes, St John Paul II and Benedict XVI, and is close to Francis.