Iftikhar Ahmed, 52, broke down at Chester Crown Court as he denied killing his daughter, or having anything to do with her murder.
His wife Farzana Ahmed, 49, also denies murdering the 17-year-old in 2003.
On Monday, the jury was told Mrs Ahmed had changed her account, claiming she saw her husband beat Shafilea on the night of the alleged murder.
She also claimed he had threatened to do the same to her and their other children if she ever asked him what happened to Shafilea after she disappeared from their Warrington home.
Asked by Tom Bayliss QC, defending, how he felt about his wife, Mr Ahmed said: "I love her to bits."
He said that had not changed, even after she changed her story.
By Nick RavenscroftBBC North of England reporter
For weeks, Iftikhar Ahmed has sat in the dock while the jury has heard the accusations against him - including by one of his own children - picked over.
Today was his chance to stand up and make his case. To say more than the two word "not guilty" plea that he offered the court at the start of the trial.
He spoke in a quiet voice. Mainly steady but at times straining with emotion - most notably when his barrister asked him about the effect on his family of his daughter Shafilea's disappearance.
"The family was devastated," he said.
Sitting 10 feet away listening is his wife of 25 years. Until this week they have spoken as one - that they both knew nothing about Shafilea's death.
This week, that ended when Farzana Ahmed changed her evidence.
Responding to a question asking whether he would ever hurt his daughter, Mr Ahmed said "no".
He was then asked if he was responsible for Shafilea's death. Again Mr Ahmed replied "no".
He then added: "We were devastated to find out that she had left home in the first place."
When he was asked how he felt when his daughter's body was found, Mr Ahmed struggled to respond, before adding in a strained voice: "We couldn't believe it when we heard."
The run-up to the trial, Mr Ahmed said, had made them "come closer" as a family.
"We have been fighting to achieve justice for our daughter Shafilea," he added.
Mr Bayliss asked Mr Ahmed if he believed he would ever know what happened to Shafilea.
Mr Ahmed responded: "We were hoping so but I don't think we ever will."
Mr Ahmed then described Shafilea to the jury, calling her "talented and athletic".
He added: "Education-wise, she was absolutely brilliant - her best subject was art, she liked making mosaics.
"She was a character in herself. Very bubbly, very talkative, everything a child should be."
Mr Ahmed told the court he "totally agreed" with his daughter's ambition to become a solicitor.
He said that it was because of her studies that he had refused to discuss a marriage proposal for Shafilea made by a "distant uncle" on behalf of his son.
He added that he did not know where the 17-year-old had got the impression she was to be "married off" from.
Mr Bayliss also asked him about his opinion of Shafilea's social life and, in particular, her friendships with boys.
Mr Ahmed said if he had known about her having a friendship with a boy, "there would not be a problem".
"If we know who she is going with and then we get to know about who he is and if she likes the person, then that's fine. It's her life," he said.
When asked by Mr Bayliss how the death and accusations had affected the family and his relationship with his wife, Mr Ahmed replied: "As a couple, it's devastating, not something we expected."
Shafilea disappeared in September 2003 and her body was found on the bank of the River Kent in Cumbria the following February.
The prosecution claims she was killed by her parents because she brought shame on the family by her desire to lead a westernised lifestyle.
The case continues.
The father of Shafilea Ahmed has told a court he was not responsible for her death.