Tournament top scorer Junior Kabananga converted Chancel Mbemba’s pass for the opener, his third goal in three games.
Kabananga hit the post with a flicked header before Ndombe Mubele doubled the lead after the break, looping the ball over the keeper amid static defending.
Kodjo Fo-Doh Laba’s tidy finish gave Togo hope, but Paul-Jose M’Poku’s free-kick secured a deserved DR Congo win.
In the group’s other game, title-holders Cote D’Ivoire were knocked out after a 0-1 defeat by Morocco, who go through as group runners-up.
DR Congo will go on to play the Group D runners-up in the quarter-finals, which will be one of Mali, Ghana or — most likely — Egypt.
Togo had to beat DR Congo to go through but the game began with ill fortune for them.
Goalkeeper Baba Tchagouni was forced off injured, and he had to be replaced by third-choice stopper Cedric Mensah as first-choice Kossi Agassa had been allowed to return home.
This was after his house was vandalised by fans angry with his performance in the previous game, a 1-3 defeat by Morocco.
After Laba’s goal, former Arsenal and Manchester City forward Emmanuel Adebayor blasted a chance for an equaliser straight at the goalkeeper.
He was also denied by a goalline clearance in injury time, but DR Congo were comfortable for the majority of the match.
Jonathan Bolingi had a goal ruled out for offside, and the striker might have wrapped the result up sooner with a shot deflected just wide.
But when M’Poku’s free-kick later swerved in off the underside of the bar, it was all over for Togo.