The liaison ended Emma and Kenneth' six-year marriage - but the actress has long let go of any feelings of resentment.
Speaking to the Sunday Times, she said she has "made her peace" with her former love rival, going so far as to describe her as a "wonderful woman".
"You can't hold on to anything like that," Emma, 54, said. "It's pointless. I haven't got the energy for it.
"Helena and I made our peace years and years ago."
Emma and Kenneth wed in 1989, two years after they first met. They were the golden couple of British cinema in the early 1990s, and were fondly nicknamed 'Ken and Em'.
They separated in 1995 saying that their work had "inevitably" led to them spending long periods of time apart.
Helena is thought to have begun her affair with Kenneth in 1994 while playing his love interest in Mary Shelley's Frankenstein, which he directed. Their relationship lasted until 1999.
Double Oscar winner Emma has previously spoken candidly about the depression she suffered following the end of her marriage.
And she said that she knew from her own bitter experience how to play her role in the 2003 film Love Actually, as a wife who suspects her husband is being unfaithful.
"I've had so much bloody practice at crying in a bedroom, then having to go out and be cheerful, gathering up the pieces of my heart and putting them in a drawer," she said.
Emma went on to say that she is similar to Helena - who appeared alongside her in 1992's Howard End and the Harry Potter films - and that may well have been the reason her ex-husband fell for them both.
"Oh we are. Being slightly mad and a bit fashion-challenged. Perhaps that's why Ken loved us both. She's a wonderful woman, Helena."
Emma, who is the only person ever to have won Oscars for both writing and acting, is now married to Greg Wise, an actor and producer who she met on the set of the 1995 version of Sense and Sensibility.
The couple have one daughter together, Gaia, 13, and a son, Tindyebwa Agaba, 26, a former child soldier they informally adopted when he was 16.
Last month, Emma admitted that monogamy was an "odd state" for humans and argued that it was too easy to be caught by the "happy-ever-after ideal".
"I do sometimes wonder about whether there are alternatives, and about whether our fury and rage and disbelief and horror about infidelity is quite realistic," she said.
"I, of course, have got the T-shirt, so I understand the feelings very well, but I think as I get older and think about long-term relationships, I do see that they can change."