Carneiro was stood down from first-team duty following a touchline row with Mourinho during the closing stages of Chelsea's 2-2 draw with Swansea City at Stamford Bridge on August 8.
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Earlier this month, her departure from the club was confirmed.
The flashpoint occurred after Carneiro and physiotherapist Jon Fearn - also subsequently withdrawn from first-team affairs - entered the field to treat Eden Hazard, with Mourinho displeased that his team would momentarily be reduced to nine men following Thibaut Courtois' red card earlier in the second half.
The FA analysed footage of the incident, including the audio recordings, following accusations the Portuguese used abusive language towards Carneiro.
The governing body said in a statement on Wednesday that it "is satisfied that the words used do not constitute discriminatory language under FA Rules".