Miller was asked about the message allegedly intercepted from her to Craig by the News of the World.
It said: "Hi. It's me. Can't speak. I'm at the Groucho with Jude. I love you."
Speaking in clear, confident voice, Miller told the court that the voicemail was not an "important declaration of love".
"The thing that's been slightly misconstrued about this voicemail message is the fact that I said I love you and that this was some incredibly important declaration of love. I've always ended my phone calls to Daniel saying 'I love you'."
Wearing black and with her blonde hair dyed brown, Miller was speaking via videolink from New Orleans in the US to a packed Court 12 at the Old Bailey.
She was shown on screen sitting next to an FBI agent in a book-lined office.
The News of the World (NotW) ran a story about her alleged affair with Bond star Craig, the court has heard.
Former NotW reporter Daniel Evans claims part of the story was sourced from hacking Craig's phone.
Miller denied the message meant she was in a relationship with Craig but she did tell the court they had a "brief encounter".
The story emerged "at a time when we had been briefly involved", she said.
Miller also confirmed she left messages on the phone of Kelly Hoppen, her former stepmother.
The court heard that Evans claimed to hear Miller crying in a message to Ms Hoppen.
Miller said: "It's a difficult time to remember. It was very emotionally raw. It is not possible for me to say whether or not with any certainty. I think I was crying a lot at the time.
"But I do not think I would have been crying in a message to Kelly Hoppen, no."
When asked about her relationship with the media by Timothy Langdale QC, for former News of the World editor Andy Coulson, she said: "It was part of my job to communicate with the media and, yes, I had some negative experiences."
The Layer Cake star said she had pleaded with a News of the World journalist to ease off her then-boyfriend Jude Law when they met at a pre-Baftas party, asking him to "give Jude a break".
She said: "I spoke to him as a human being, making clear that this was an off-the-record conversation.
"This was a conversation between two human beings, not an actress and a journalist. I appealed to his better nature and this was then abused.
"I probably said 'He's one of the nicest, kindest people I know and you are misrepresenting him, please stop it'."
When asked if she had ever courted publicity, she said: "Absolutely never, not once. Never ever.
"Hand on my heart, I've taken an oath."
Miller said she was not aware that anyone associated with her or her then boyfriend Law was communicating with the NotW in 2005.
There was laughter in the court when Miller was questioned by defence lawyer Mr Langdale about her message to Craig which ended "I love you".
She said: "You just told me you love me and I interrupted you."
There was also laughter as the actress struggled to remember the date of her sister Savannah's wedding.
She joked: "This is a terrible test."
Miller said she regretted that information about her had been analysed in the media during the course of the trial.
Thanking her for giving evidence, judge Mr Justice Saunders told her: "I am very sorry what has gone on in this court and reported in the press has caused you distress. We have tried to limit what has been said in court."
Coulson 46, a PR consultant of Charing, Kent, denies conspiring to hack phones and conspiring to commit misconduct in a public office.
All seven defendants, including former Sun and NotW editor Rebekah Brooks, deny all the charges against them.