The world No.1 did not have it all his own way against the world No.255, with the first set featuring just three service holds.
But Djokovic claimed four breaks to Molcan's three to take the opener and did not let his advantage slip in front of his home crowd.
He negotiated a similarly tricky second set to prevail 6-4 6-3, with attention now turning to the second grand slam of the year after Djokovic won the Australian Open back in January.
After a resilient performance in the first set as he twice came back from a break down, Djokovic was able to enjoy a slightly less frenetic path to victory in the second.
He broke down a more obdurate Molcan for a 4-2 lead, only for the Slovak to hit straight back.
But Djokovic was not to be denied and immediately claimed another break, which he consolidated to delight his adoring public.
Victory in what was Djokovic's first final on home soil since 2011 means he now has 83 ATP singles titles to his name, with three of them coming at this event.
It also caps a positive period of preparation for a tilt at a second French Open title, with Djokovic having reached the final in Rome this month only to lose to Roland Garros favourite Rafael Nadal.
Nadal and Djokovic could meet in the semi-finals this year in Paris, where the Serbian was thrashed by the King of Clay in three sets in the 2020 final.
Djokovic will start his campaign to add to his 2016 French Open success when he faces Tennys Sandgren in the first round.