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, holders Ivory Coast were knocked out after a 1-0 defeat by Morocco, who go through as group runners-up.
DR Congo 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 and the game began with ill fortune as goalkeeper Baba Tchagouni was forced off injured.
He had to be replaced by third-choice stopper Cedric Mensah as first-choice Kossi Agassa had been allowed to return home after his house was vandalisedby fans angry with his performance in the previous game, a 3-1 defeat by Morocco.
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