Ben Reeves scored the only goal of the game, early in the second half, as Dover's FA Cup run came to an end at the Stadium MK.
The League One side had not been in the best of form, losing seven of their previous nine games, but were too strong Dover of the Conference South.
Dons' manager Karl Robinson had warned his players they dare not lose to the non-League side, and there was little danger of an upset as MK Dons dominated throughout.
Match summary
MK Dons 1-0 Dover Athletic
FA Cup Second Round
Saturday 7 December 2013 Stadium mk, Milton Keynes
Att: 4,060
Jason Banton went close with a couple of early shots for the home side on his return to the side, but was replaced at half-time by George Baldock. Robinson's switch paid dividends five minutes into the second half when Baldock broke down the right before cutting the ball back for Reeves to fire home from 12 yards.
That goal proved enough, although Baldock went close twice and Dover defender Sean Raggett almost scored an own goal, with the ball hitting a post to spare his blushes.
But Dover could have forced a replay in the 70th minute when the ball dropped invitingly for Nathan Elder, only for the striker to shoot over the bar from close range.
David Martin, returning in the MK Dons goal after a four-game absence, was replaced in the closing stages by Ian McLoughlin but the substitute keeper had little to deal with as the League One side progressed to the third round.
MK Dons: Martin (McLoughlin 77), Lewington, Hodson, Williams, Spence, Gleeson, Smith, Reeves, Banton (Baldock 46), Carruthers (Galloway 77), Bamford
Subs not used: Flanagan, Rasulo
Dover Athletic: Walker, Stone, Wynter, Kinnear Jnr (Orlu 90), Raggett, Forbes, Modeste (Bakare 57), Rogers, Elder, Cogan, Murphy (Charles 85)
Subs not used: Hook, Kamara, Woodall, Carew.
