McClean was furious that Trapattoni did not bring him off the bench on Friday night as the Republic struggled to a 2-1 win over eastern European minnows Kazakhstan.
In an apparent broadside at Trapattoni's refusal to call on his services, the Sunderland winger tweeted: "Delighted as a fan we got the the win.. Personal level fuming #f****njoke #embarrassing.''
Trapattoni spoke to McClean about the tweet, which the midfielder quickly deleted, and the player issued a full apology on the micro-blogging website on Saturday afternoon.
He wrote: "i apologise for my tweet last night, it was stupid, disrespectful and i let my frustration get the better of me which still aint an excuse.''
Trapattoni then also spoke to McClean in front of the whole squad before the player apologised to his team-mates in the room. Trapattoni had considered dropping McClean from his squad for the outburst, but the former Derry City man's apology means he has been retained for the Emerald Isle's international friendly against Oman at Craven Cottage on Tuesday.
The tweet once again raises questions about Trapattoni's relationship with some of his players. Having seen Damien Duff and Shay Given retire from international football this summer, the Italian was then disappointed by the actions of Darron Gibson, who refused a call up for these two games.
And last month Wolves utility man Kevin Foley turned down the chance to play for his country in their friendly against Serbia and vowed never to play for Trapattoni again because he felt the Italian "betrayed" him by excluding him from his European Championship squad.
Kevin Doyle has tried to play down talk of unrest and insisted the whole Republic squad are behind Trapattoni, whose position would have been under intense pressure had Doyle and Robbie Keane not scored two late goals to snatch all three points on Friday night in the former Soviet republic.
"Everyone is together," Doyle said. "Everyone respects the manager 100% and there is no other scenario. Honestly, it's the same as any squad I have been involved in with Ireland. Everyone is entitled to their opinion and feeling but as far as I can see everyone is right behind the manager and hopefully that win will ease the pressure on us."