Sir Alex Ferguson's successor got the new era off to a winning start as the Red Devils overcame Championship opposition at Wembley.
Van Persie opened the scoring in the sixth minute with a brilliant header into the bottom corner before sealing the victory in the second half with a deflected strike.
United was far from convincing against the FA Cup holder - now playing in the Championship - but Moyes will be relieved to have successfully won the trophy after leading his side out at Wembley for the first time.
Sir Alex Ferguson either won or shared the Community Shield nine times and it would have been a welcome relief for Moyes to focus on matters on the pitch following an unsettling summer of transfer speculation.
The Scot raised a few eyebrows before kickoff as he said that Wayne Rooney will feature for England against Scotland on Wednesday but suggested that the striker will not play when United starts its title defense against Swansea City.
While Rooney has dominated United's preseason, the new manager knows that he can rely on Van Persie as the leader of his attack this season, with the Dutchman selected to lead the attack as winger Wilfried Zaha was handed his debut.
The first official goal of the Moyes era arrived via Van Persie after just six minutes when last season's Premier League top scorer rose high just inside the penalty area to meet Patrice Evra's cross and plant a fantastic header into the bottom corner.
United, though, lacked vibrancy in possession and it was clear why Moyes has made signing a central midfielder his top priority this summer as the club failed to create clear chances in the first half.
Indeed, Wigan would have been the happier of the two sides at the break as the Championship team defended stoutly and threatened on occasions on the break, with Grant Holt poking a volley just wide of the post.
There was little change in the pattern of the game after the restart until van Persie scored his second goal of the game in the 59th minute.
The United star worked the ball on to his left foot after collecting Danny Welbeck's pass before firing towards goal from the edge of the penalty area. The ball appeared to be heading straight at Wigan goalkeeper Scott Carson before it struck the boot of James Perch and flew into the corner of the net.
Moyes's men were content to keep possession and see the game out after doubling the advantage in hot conditions under the north London sun before Nemanja Vidic lifted the trophy.