Ciaran Toner scored his first goal of the season to lift Leyton Orient into the top half of the table and stretch their unbeaten home run to six matches.
The defeat kept Darlington in the bottom two and was rough justice on the visitors who missed a string of chances.
O's boss Martin Ling admitted: "I won't try and pretend that was a performance. Darlington had 70 percent of the play.
"It's the worst display since I have been manager. Darlington were the better side but we got out of jail.
"I can't even say we defended well as Barry Conlon missed three guilt edge chances and if the players think that's good enough they are mistaken." Darlington manger David Hodgson was distraught and said: "We are second from bottom because we are not scoring goals.
"In the second half we were the better side and kept Leyton Orient firmly on the back foot. We had so many chances and so much of the ball but we have to have the desire to score goals." Leyton Orient took the lead after surviving early pressure when Tom Newey's through ball split the visiting defence and Toner fired the ball through keeper Michael Price's legs from 12 yards.
Orient, who have had nine players sent off this season, could of been reduced to ten men shortly afterwards when striker Lee Thorpe appeared to elbow Matthew Clarke - but escaped with a booking.
The early goal failed to settle Orient's nerves and Darlington went close to levelling before the break as Conlon saw one shot blocked by defender Matthew Joseph and then keeper Glen Morris tipped another effort away.
Darlington took a vice like grip after the break and although O's midfielder Justin Miller twice went close on rare raids the Quakers should have levelled as Conlon headed wastefully over on two occasions while Lee Matthews also had two good chances.