The FA confirmed that the incident in Sunday's Premier League clash at the DW Stadium was seen by at least one of the match officials - even though referee Mark Halsey was unsighted - meaning that retrospective action cannot be taken.
Haidara suffered potentially serious knee ligament damage after the challenge by 21-year-old McManaman, but no action was taken against the Wigan player during the match.
The FA said in a statement: "The FA can confirm that no action can be taken against Wigan's Callum McManaman retrospectively following his side's game against Newcastle United on Sunday 17 March 2013.
"Following consultation with the game's stakeholders (the Premier League, the Football League, the Professional Footballers' Association, the League Managers' Association, Professional Game Match Officials Limited and the National Game) in the summer, it was agreed that retrospective action should only be taken in respect of incidents which have not been seen by the match officials.
"Where one of the officials has seen a coming together of players, no retrospective action should be taken, regardless of whether he or she witnessed the full or particular nature of the challenge. This is to avoid the re-refereeing of incidents.
"In the case of Callum McManaman, it has been confirmed that at least one of the match officials saw the coming together, though not the full extent of the challenge. In these circumstances retrospective action cannot be taken.
"The principal objective behind the not seen policy is to address off-the-ball incidents where match officials are unlikely to be in a position to witness misconduct."
Newcastle's managing director Derek Llambias expressed disappointment at the FA's decision and said the club would make approaches to change the disciplinary process.
Llambias also questioned Wigan chairman Dave Whelan's claim that the challenge was "fair".
He said in a statement: "We are disappointed to learn that the FA is not going to charge the Wigan player.
"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.
"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.
"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."
In relation to Whelan's remarks, Llambias added: "I have the greatest respect for Dave, who has been in the game for a long time as a professional footballer and now owner. I am also aware that Dave's career was cut short due to injury.
"I am therefore disappointed and surprised by the comments he made yesterday, in particular his assertion that the tackle by Callum McManaman 'was a fair challenge'.
"It is our strongly held opinion that the tackle on Massadio was extremely dangerous and is the type of challenge that has the potential to cause serious harm and such was the force, and reckless and dangerous nature of the challenge, even end a player's career.
"It was not a fair challenge. This view is shared by countless former players, referees and well-respected media commentators. Indeed it appears to be only Dave Whelan who takes a contrary view."
Llambias said Haidara had had a scan on Monday and will have another one next week to assess the extent of the damage.
The FA confirmed that Newcastle's assistant manager John Carver and Wigan coach Graham Barrow have been charged with misconduct by the Football Association following a clash at half-time in Sunday's match at Wigan.
They have until 4pm on Friday to respond to the FA charge.
In other words "We at the FA are looking desperately for ways to avoid actually doing anything useful. We have found a loophole that allows us to do just that."- Goonawan