Latics forward McManaman escaped punishment over a reckless lunge on Toon defender Massadio Haidara during Wigan’s controversial 2-1 win at the DW Stadium last weekend.
Referee Halsey is understood to have missed the incident as his view was obscured, but his assistant Matthew Wilkes had a clear line of sight and did not signal for an offence.
FA have confirmed they cannot take retrospective action, which can only happen if all the officials fail to see the incident.
The full extent of Haidara's injury is not yet known, as medics wait for the swelling to subside, but the Frenchman is expected to miss several months with knee ligament damage.
Newcastle reacted furiously to the decision to let the Wigan forward off the hook, calling the FA’s disciplinary processes “not fit for purpose”.
The club said they would not let the issue lie, with The Telegraph saying they could sue Wigan over the challenge – just as they were sued in 2009 when then-captain Kevin Nolan injured Everton striker Victor Anichebe.
Meanwhile, The Sun reported that Halsey received a death threat from an irate fan.
"Mark was made aware of one particularly vile message asking for his address and claiming he deserved a death threat,” the newspaper reported a friend of Halsey as saying.
"Mark loves refereeing and is consistently one of the best in the game but after something like this he is left wondering whether it is all worth it.
"He didn't even sleep on Sunday."
Newcastle, meanwhile, released a furiously-worded statement after receiving the news that McManaman would not be punished by the FA.
“We are disappointed to learn that the FA is not going to charge the Wigan player,” Magpies managing director Derek Llambias said.
“We were first notified of this decision by a national media outlet who received notification from the FA confirming the decision.
“This was prior to anyone from the FA having the courtesy to contact the club to let us know.
“It is clear from this decision that the current disciplinary procedures are not fit for purpose. Newcastle United, along with other clubs, have had players suspended for incidents reviewed after the game.
“Whilst not trivialising these incidents, they were not, in our opinion, of the seriousness of Callum McManaman's tackle on Haidara.
Llambias added that the club would take the matter further, and would lobby the FA and Premier League to change their disciplinary processes.
“We will now be making a strong representation to the FA and the Premier League to see how a more appropriate, fair and even-handed disciplinary process can be introduced at the earliest opportunity to prevent incidents of this nature going unpunished in the future.
“Whilst we understand that the current procedures give the FA limited options, it cannot be correct that the most serious offences - those which have the potential to cause another player serious harm - can go unpunished, even if the original incident was seen by match officials.”