The Latics player, enjoying his first Premier League start on Monday, caused outrage with a reckless knee-high challenge on substitute Massadio Haidara.
He escaped punishment while referee Mark Halsey sent off furious Newcastle assistant manager John Carver - who twice had to be restrained as he tried to confront McManaman at the end of the first half - and Wigan coach Graham Barrow in an unseemly fracas.
"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," the FA stated.
"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."
It is believed that Halsey's view was blocked but that his assistant Matthew Wilkes saw the challenge.
The FA went on to say that the main purpose of the 'not seen' rule is to address off-the-ball incidents.
Newcastle reacted furiously to the decision to let McManaman off.
"We are disappointed to learn that the FA is not going to charge the Wigan player," Newcastle 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."
Meanwhile, the FA has confirmed that Newcastle assistant manager John Carver and Wigan coach Graham Barrow have been charged with misconduct following a clash over the incident at half-time.
Carver was angry with McManaman and Barrow also got involved in the fracas as the players left the field.
Both men were sent to the stands for the second half of the match, which Wigan won 2-1.
Carver and Barrow have until 4pm on Friday to respond to the charge.