It is believed there are no other people who are being investigated in relation to Ms Meagher's disappearance.
Homicide detectives arrested Bayley at his home at 2.30pm (AEST) on Thursday.
He was charged about 2.30am local time this morning and appeared before an out-of-sessions court hearing in the St Kilda Road police complex in Melbourne.
In a hearing that lasted no more than a couple of minutes, Bayley barely spoke, saying "yes'' in a gruff voice to the question of whether he understood the charges against him.
He said "no'' when asked if he wanted the charges against him read out.
The bail justice told him that because the charges against him were rape and murder she could not grant him bail.
He was remanded to appear in the Melbourne Magistrates Court later this morning.
Dressed in jeans, runners and a tight blue T-shirt, Bayley kept one hand clapped over his mouth throughout his brief appearance.
The muscular man with short, blond hair made no show of emotion throughout his brief appearance.
It is believed Bayley helped officers locate Ms Meagher's body, which was found in Gisborne South about 1.45am on Friday.
Officers are continuing to conduct a forensic analysis at the scene.
CCTV footage critical
The breakthrough in the case came after police released CCTV footage showing the last known images of Ms Meagher, as she walked outside a bridal dress shop on Brunswick's Sydney Road - within 450 metres of her home - about 1.40am on Saturday.
In the CCTV footage released on Wednesday, Ms Meagher could be seen speaking with a man in a blue hooded jumper outside the store.
She then speaks to her brother on her mobile for two minutes, walks out of view of the camera, and had not been seen since.
Ms Meagher, who moved from Ireland to Melbourne three years ago, had left Bar Etiquette on Sydney Road at 1.33am after drinking with ABC colleagues.
But police say she never completed the five-minute walk to the flat she shares with her husband, Thomas.
Her handbag was found in a nearby laneway, which had already been searched by police, on Monday morning.
Mr Meagher had been desperately seeking answers to her disappearance.
"She's my best friend,'' he told media this week.
Colleagues mourn loss
Jill Meagher's distressed colleagues at the ABC are describing her as a witty, vibrant young woman who became an innocent victim when she had her whole life ahead of her.
"On behalf of Local Radio Victoria, we are deeply saddened and pained by the tragic news of the death of our friend and colleague Jill Meagher,'' the broadcaster said in a statement on Friday.
"Our thoughts go out to Jill's family and friends, so devastated by the passing of this wonderful young woman.''
- AAP
