James, 31, feared his wife would find out about the liaison and told bosses: “It’s her or me.”
Emily, 29, who played schoolgirl Charlotte “Big Jugs” Hinchcliffe in the hit comedy, only learned she was not needed on the eve of its ten-year reunion.
The pair’s fallout casts doubt on Emily appearing in the show again, as bosses consider a new series.
A source revealed: “Emily got a call from producers 24 hours before she was due on set.
“They were deeply embarrassed and apologetic. They had to explain that James had asked she be taken off the show.
“The pair had a couple of cheeky snogs back in the day when they were both single.
“But James didn’t want it to become a major issue on the reunion, or with his wife Clair.
“The kissing meant nothing to Emily and has never been an issue for her. She was very taken aback to be told she wasn’t needed, and genuinely gutted.
“She thought everything was good to go, and was looking forward to reuniting with the guys.”
James played foul-mouthed, sex-obsessed Jay Cartwright who famously lied about past conquests.
He snogged Emily before he met his wife as the pair filmed early episodes of the show.
James is also said to have had reservations over Emily’s stint on I’m A Celebrity.
She finished runner-up to Harry Redknapp in December.
Sources say James told producers her appearance in the jungle was not in keeping with The Inbetweeners’ cult appeal.
The source added: “Emily heard James had slagged her off about I’m A Celebrity, saying it was tacky and not ‘on brand’ — which she understandably found patronising.
“Emily never wanted this to come out. She just wants to rise above it and move on.
“She has lots more exciting things in the pipeline which will be a bit of a ‘two fingers up’ to The Inbetweeners.”
The Bafta-winning comedy originally aired on E4 for three series ending in 2010, and became the network’s most watched show.
Eight years ago the cast filmed a Comic Relief special, and in 2011 and 2014 two smash movies were made, grossing more than £120million between them.
Fans were scratching their heads at Emily’s absence from January’s two-hour, one-off special called The Inbetweeners: Fwends Reunited.
It featured all four lads — James, Simon Bird (who played schoolboy Will McKenzie), Joe Thomas (Simon Cooper) and Blake Harrison (Neil Sutherland), plus Greg Davies (their headteacher Phil Gilbert) and Emily Head (Simon’s love interest Carli D’Amato).
Actresses from the first film also appeared despite having smaller roles than Emily, a TV series regular.
Jessica Knappett (Lisa), Lydia Rose Bewley (Jane) and Lauren O’Rourke (Nicole) joined the lads plus reunion host Jimmy Carr.
Last month during a podcast recording, Emily hinted one cast member was behind her surprise omission.
When the host mentioned James’s name she shouted out “James F***ley”.
And in December Emily revealed she had been cut but claimed she had no idea why.
She told Capital FM: “Unfortunately, I don’t really know what happened there.
“I was booked to do it, was very much looking forward to doing it and then the day before I was told I was no longer needed for it.
“It’s all right. These things do happen and I think they just decided to go a different route with it.
"I don’t know, or it was to do with production timings and things.” Critics panned the special as “painfully bad” and a “disappointment”.
Fans moaned that it was more a chat show that reviewed past episodes rather than showing any new material.
Afterwards James tweeted to say he felt “pretty hated right now”.
He added: “I’m sorry to anyone who feels let down with last night’s show.
"I’m especially upset as it really is the fans that made The Inbetweeners a success, it certainly wasn’t me.
"I might do an explanation video on my YouTube, or might just leave it & move on. #sorry.”
Emily and James’ snogging antics took place before James met his wife, Scottish model Clair Meek.
The couple, who have sons Harrison and Jude, wed near Edinburgh in 2012.
Guests included his cast mates and EastEnders star Danny Dyer.
Emily has previously dated One Direction hunk Harry Styles.
In October it emerged she’d had a fling with Strictly love rat Seann Walsh while he was still dating actress Rebecca Humphries. Comic Seann had told Emily he was single at the time.
Three months ago The Sun on Sunday revealed Emily been accused of a secret fling with her married pro skater partner Fred Palascak on 2010’s Dancing On Ice.
Emily dated McFly’s Dougie Poynter after splitting from her model boyfriend of five years, Jack Vacher.
Last week she signed a lucrative deal to launch a fashion line.
Her spokesman declined to comment last night.
Jokers' top gags
JAY: “On holiday in Spain, me and me mate got on a pedalo and ended up in Africa.”
WILL: “I’m a principled man, and one of those principles is I’ll do literally anything a girl asks me to do.”
JAY: “Bring your wellies, because we’re going to be knee deep in clunge!”
NEIL: “What’s this pesto stuff? Is it for humans?”
SIMON, JAY and NEIL: “Bus w***ers!”
SIMON to WILL: “You’ve only kissed three girls. Your type is ‘anyone who’ll let you’.’”
JAY’S DAD: “There’s plenty more fish in the sea — and Jay’s harpooned himself a whale.”
NEIL: “I stopped believing in God when I realised it was just ‘dog’ spelled backwards.”
NEIL: “I got this new app called Grindr and immediately found loads of new friends.”
WILL having ingested cannabis: “I need you to call an ambulance, or failing that, my mummy. I really want my mummy because, and I’m not being dramatic, but I think I might be dead. Mummy or an ambulance.”
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