A Professional Game Match Officials Limited statement on Saturday evening revealed the apology after Marriner dismissed Gibbs for a foul committed by Alex Oxlade-Chamberlain which resulted in a penalty in the 17th minute of the match.
The worrying thing was - Oxlade-Chamberlain told the referee HE handled the ball - but the referee refused to admit he was wrong.
All he had to do was get Gibbs back on the field. But he restarted the game KNOWING he was wrong.
Statement: "Andre is an experienced referee and is obviously disappointed that an error of mistaken identity was made in this case.
"Incidents of mistaken identity are very rare and are often the result of a number of different technical factors.
"Whilst this was a difficult decision Andre is disappointed that he failed to identify the correct player.
"He expressed his disappointment to Arsenal when he was made aware of the issue."
The Football Association subsequently confirmed that Arsenal, or the governing body themselves, could appeal the sending off on the grounds of "mistaken identity".
It continued the debate for the use of television replays.
The decision would not have happened under UEFA's extra-officials policy, according to a spokesman for president Michel Platini.
Pedro Pinto, the chief of press for Platini, said an extra referee on the by-line would have identified the correct culprit.
Pinto wrote on Twitter: "What confusion at Chelsea-Arsenal with the pen decision. That's why over 30 European countries have endorsed UEFA-backed 5 officials system.
"With an additional assistant referee on the end line, referee would not have got that sending off wrong. Technology is not the answer..."
Pinto claimed that "more eye balls" were the key to improving referee decision-making rather than technology alone.
The Barclays Premier League has employed goal-line technology for the first time this season - which would not have aided Marriner's decision at Chelsea because it determines whether a shot has crossed the line only.
Pinto added on Twitter: "More eye balls are the answer. GLT helps with goal line decisions, but five officials system gives referee more angles of vision. It's not one vs the other."
The only saving grace on this occasion was that the decision did not appear to impact on the result and it is likely that Oxlade-Chamberlain will serve the suspension if Arsenal appeal or the Football Association intervene.
"Clubs can appeal mistaken identity to The @FA, although The @FA can pro-actively review also," an FA tweet read.
There is a precedent for the decision to be changed after Sky Bet League 1 side Preston had the wrong man sent off against Port Vale in November.
Striker Joe Garner was suspended retrospectively for three games after midfielder Neil Kilkenny had mistakenly been sent off.
BUT IF TV FOOTAGE IS GOING TO BE USED TO PROVE IT WAS OXADE-CHAMBERLAIN WHO HANDLED - IT ALSO SHOWS THE BALL WAS GOING WIDE AND HE DIDN'T DESERVE A RED CARD!
WILL THE FA CONSIDER THAT? I DOUBT IT!