Apart from making this year's All-Australian team, Griffen also won his second club best-and-fairest award.
Boyd had led the Bulldogs for the past three seasons, but missed nine games this year because of injury.
Griffen, 27, has played 183 games for the 'Dogs since they took him with the No.3 pick in the 2004 national draft.
"Its a huge honour to lead this club, a club I love dearly," he told the club website.
"I'm extremely humbled, that the coaches, staff and my teammates nominated me as the person to captain the club."
Griffen filled in as captain this season when Boyd was injured.
Boyd then encouraged him to take the job full-time.
"Matthew has been a great leader of this club, particularly through some challenging times over the past three years where he shouldered some enormous responsibility both on and off the field," coach Brendan McCartney said on the AFL website.
"We see Ryan as the right person to help take this club forward and we look forward to seeing him continue to grow as a leader, player and person."