Peel, who has won 64 caps and was the 2005 Lions Test scrum-half in New Zealand, was a shock omission from Wales coach Warren Gatland's 28-man Six Nations squad.
Peel failed to win the vote ahead of Gloucester's Gareth Cooper and Ospreys number nine Mike Phillips, but Jones has no doubt he will make a return at some point.
"I know a few of the boys have been in contact with Dwayne," said the skipper.
"Knowing him as I do, I know he will knuckle down, work hard and wait for his opportunity again.
"Every Welsh squad I've been involved in in recent years has had Dwayne Peel in it. He is a huge asset to the squad, on and off the field.
"I am certain we haven't seen the last of him."
Wales have been installed as clear favourites to land a second successive Six Nations crown, and third in five seasons.
They were the only northern hemisphere country to beat Tri-Nations opposition during last November's autumn international schedule, defeating Australia in a Millennium Stadium thriller.
And with match-winning players like Phillips and Gavin Henson back from injury after missing the entire autumn series, Gatland's men could justify their bookies' label.
Gatland said: "The tag of favourites is something you can't hide away from. We've got to address it and accept it.
"We are Six Nations champions and teams are going to be gunning for us. We would like to think that gives us some confidence and self-belief.
"We feel we are one of the best teams in the northern hemisphere, and the challenge for us is not to run away from it, but to embrace it.
"If we want to be considered one of the best teams in the world, there is a going to be an expectation on us to perform from game to game and tournament to tournament."