Portugal international Moutinho was in inspired form for Porto, who were already assured of a last 16 place.
He found Argentine playmaker Lucho Gonzalez for the opener on 20 minutes through some textbook passing play, blasted the second himself from a free-kick in the second half and finished with a wonderful backheel to set up Silvestre Varela's third.
Porto, unbeaten in all competitions this season, will win the group if they take a point from their final game next month away to second-placed Paris Saint-Germain.
"It was another good match. We have been consistent and aggressive. I am pleased but we still want to finish top of the group and do so playing good football," said Porto coach Vitor Pereira.
The hosts commanded possession from the start but the visitors almost caught them by surprise when Brazilian-born forward Sammir blasted a diagonal shot against the post from a quick counter-attack.
Dinamo, still looking for their first goal of the group stage, were then caught out when Porto pierced their frail defence with a quick first-touch exchange between Moutinho and Colombian striker Jackson Martinez that ended with Gonzalez firing into the net with his left foot from just inside the box.
Fatos Beqiraj almost poked in an equaliser in for the Croatian champions after a corner but Varela cleared off the line.
Porto strolled through the second half and extended their lead when Moutinho swerved in a sweet free-kick that left keeper Ivan Kelava rooted to the spot.
He rounded off his man-of-the-match performance with a backheel to set up Varela's third five minutes from time.
Porto top Group A with 13 points, ahead of PSG on 12, Dynamo Kiev with four and Dinamo yet to get off the mark.
