Starting the stage 53 seconds down on Quintana and 14 seconds behind Vincenzo Nibali (Bahrain-Merida), Dumoulin needed a performance as commanding as his stage 10 time trial victory where he finished over two minutes ahead of the duo.
Dumoulin covered the 29.3km course through the streets of Milan in 33 minutes and 23 seconds, just 15 seconds behind stage winner Van Emden. He was the virtual leader by Quintana's second time check.
The Dutchman's final time was one minute and 24 seconds faster than Quintana's, pushing him to his 31 second lead overall. Nibali performed strongly but still finished 54 seconds in arrears, leaving him third overall behind Dumoulin with a 40 second deficit.
It was an emotional win for Van Emden who blitzed the course in an average speed of more than 53 kilometres per hour.
"I'm the happiest man on earth," he said. "I am so happy that I can finally win after all my second places. I have been sitting on the hot seat for a long time and most times, someone else was faster.
"Finally, I’m the one who can shout how happy I am."
But of course, the day belonged to Dumoulin who was nervous until Quintana finally crossed the line.
"I didn't know any time gaps during my TT," he said "I just wanted to focus on my own (and asked) my sports director (to) tell me when I was safe. And he said to not take any more risks around the corners, and he said this already at half way. I was like, OK, I must be really safe.
"Then when I crossed the line, everyone said "you won, you won" and I looked at the TV... (I only led by) three seconds. I was so angry at everyone, 'how could you say that I'm safe?,'
"I won a very special race. It's amazing when you see all the names on the trophy. I don't feel myself like a champion, but I almost feel like it when I see my name on the trophy. It's very special."
"I will be very tired tomorrow," he said of the team's celebrations.
The 100th Giro d'Italia winner also joked with reporters after a journalist said "you made history and not because you s*it in the woods."
"I still made history with s*itting in the woods," he laughed.
Dumoulin is the first Dutchman to win the Giro d'Italia and only the third to win a grand tour after Jan Janssen's 1967 Vuelta a Espana and 1968 Tour de France victories and Joop Zoetemelk's 1980 Tour de France win.