The 67-year-old was handed a three-year contract in a controversial appointment by Magpies owner Mike Ashley last summer - and was tasked with identifying new playing talent for manager Alan Pardew.
However, Kinnear has quit for unspecified reasons after less than eight months in the job.
There will be no new appointment in the short term although there is speculation that former managing director Derek Llambias could return to St James' Park.
Llambias, who had previously conducted transfer business, left the club within days of Kinnear's arrival but he is reportedly back on good terms with Ashley.
There was only one addition to Newcastle's senior squad after Kinnear was appointed last summer, a loan deal bringing striker Loic Remy to the club from Queens Park Rangers.
The only permanent addition he engineered during his return to the north-east turned out to be teenage prospect Olivier Kemen from Metz.
January's transfer window proved just as frustrating for Newcastle fans waiting to see their squad boosted, with just one player joining - striker Luuk de Jong from Borussia Monchengladbach, again on loan.
There was also one huge void left to fill, with the club allowing influential midfielder Yohan Cabaye to join Paris Saint-Germain for a fee of around £20m.
They were interested in signing Lyon's Clement Grenier and Montpellier's Remy Cabella but neither deal was ever consummated.
Worse would follow in their first fixture after the window closed when they were thrashed 3-0 by fierce rivals Sunderland at St James' Park, with Kinnear and Ashley nowhere to be seen as Pardew bore the brunt of a furious backlash.
Former Newcastle striker Alan Shearer has expressed dismay at the way the club is conducting itself off the field after Kinnear's resignation.
"That's life at Newcastle United," he said.
"I shouldn't say I'm surprised but I was surprised in the first place when he was announced director, particularly the way the news was broken when Joe himself announced it on the radio when he got some of the players' names wrong.
"What has he been there now, about seven months? And two players have come in, albeit both players on loan.
"Maybe it's Newcastle's way of trying to say that the performance on Saturday wasn't good enough and why they didn't get any new players in, maybe that's one of the reasons.
"But they can only get players in if there's one man prepared to sign a chequebook."