Cecchinato converted four out of eight break points to beat his Australian opponent in an hour 47 minutes. The world number 92 became the first lucky loser to win a title since Leonardo Mayer triumphed in Hamburg last July.
"I lost Sunday (in qualifying) and now I won the tournament. It's amazing for me," the 25-year-old Cecchinato said. "Maybe it's a dream, I don't know."
ATP Monte Carlo
'Atmosphere of a cemetery' - Paire vents frustration again after Monte Carlo loss
Cecchinato broke Millman early in the first set to race into a 4-2 lead, but the 28-year-old Australian dragged himself back into the match by winning the next three games.
Cecchinato saved a set point on his serve while trailing 5-4 before regaining his composure to take the first set.
Millman took a 4-1 lead in the second but Cecchinato fought back in style to claim victory.
"Today is a special day because I won the first title of my career," he said. "I'm very happy."
Millman reached the final earlier on Sunday after winning the final set of a 2-6 7-6(3) 7-6(5) victory over last year's runner-up Aljaz Bedene. The semi-final was suspended on Saturday due to darkness.
ATP Monte Carlo
Nadal shrugs off fitness concerns ahead of Monte Carlo return
Kudermetova and Kovinic into Charleston Open final