Slovakian Molcan, in search of a first triumph at main tour level, came flying out of the blocks, but ultimately Belgian Goffin's experience showed as he recorded a 3-6 6-3 6-3 victory.
World number 65 Molcan, who defeated Goffin in the first week of the season in Melbourne, was in early control of this meeting in Marrakesh, a set to the good and serving at 2-1 up in the second.
However, former world number seven Goffin responded from that point onwards and did not look back as he won in one hour and 58 minutes.
Goffin feels he can take confidence from this success into the rest of the clay-court segment of the 2022 season.
"I'm very happy, proud of my week. It was not easy, a lot of tough matches," Goffin said. "But at the end, I have my sixth title, here in Marrakesh. It gives me a lot of happiness and confidence for the season on the clay.
"It was the case twice before that match that I lost the first set and I always stayed calm the whole week to turn it around. It was the case again today, because he was playing well.
"He was better than me in the first set, and then I managed to play better and better, serving better, being more aggressive in the middle of the second. I was the better player [after that]."
Quoted on the ATP website, Goffin said: "I was playing even better in the third set, so I'm really happy the way I finished with another break [and] a good match point. I didn't want to serve for the match, I preferred to finish with a break."
Molcan reflected on a positive week in Morocco that saw him most notably beat top seed Felix Auger-Aliassime.
"It was an amazing week for me," he said. "I won a lot of matches and enjoyed it very much."