Salman's father Salim Khan and his mother Salma arrived in the city in the afternoon and went straight to the Jodhpur Central Jail to meet Salman, who is serving a prison term for hunting an endangered deer in 1998.
The actor, who can only meet three visitors in 15 days according to jail rules, had met brother Arbaz, sister Alvira and girlfriend Katrina Kaif on Sunday.
His parents sought to meet their son on the grounds of his mother being ill.
However, they were not allowed in.
"Visitors are allowed between 3-5 p.m. Since they came late, we did not grant them permission," said Ota Ram, a senior jail official.
Sohail Khan, the actor's brother, said: "I along with my father and mother went to the jail with a request to allow us to meet Salman, but the authorities refused to allow us and as the time had elapsed."
The family spent over 30 minutes inside the jail.
Earlier, the jail authorities had said that no special treatment would be given to the celebrity prisoner.
"Three persons would be allowed to meet him in 15 days and we would follow the jail manuals in his case too," Ota Ram had said.
A source close to Salman's family said that his sisters Alvira and Arpita might try and seek permission from the court to tie a rakhi on him in prison Tuesday on the occasion of Raksha Bandhan.
Now with Salman's parents here, almost all of the actor's family is camping in Jodhpur. They are hoping to take him back on Wednesday when the Rajasthan High Court is to hear his revision and bail plea.
According to a source in the jail, the popular actor is not eating much, is feeling troubled by the mosquitoes there and had spent a sleepless second night in prison.
The actor is keeping himself busy sketching, a hobby he is quite good at.
Earlier in the day Salman's counsel had presented his petition before the court, seeking that it be heard on an urgent basis Monday itself.
The court, however, said it would hear his petition Wednesday.
Salman has already spent two nights at the central jail in Jodhpur.
In his plea, Salman has stated that there was no evidence against him in the case and his driver Harish Dulani's testimony in court was not trustworthy, as he has been changing his statements frequently.
He has been convicted of hunting a chinkara deer at the Ghoda farm near Jodhpur on the night of Sep 28, 1998, while filming Sooraj Barjatya's blockbuster "Hum Saath Saath Hain".
According to Mahipal Bishnoi, counsel for the Bishnoi community who consider the deer a sacred animal and have filed the case: "The court can call for records on Wednesday or grant him bail."
If the court calls for records from the lower courts, then the case can go on till Sep 3, he added.
Salman, who is prisoner No. 343 of Jodhpur central jail, once again had gur (jaggery), chana (roasted gram) and tea for breakfast Monday.
"He got up early in the morning, did some exercises and was offered the usual breakfast," the source in the prison told.
Meanwhile, some of his ardent fans prayed at the dargah of Sufi saint Khawaja Moinuddin Chisti in Ajmer, hoping for his early release.
On Friday, the district and sessions court here had dismissed the actor's plea against the five-year jail term handed by the chief judicial magistrate's court.
In April last year, Salman had filed an appeal in the district and sessions court against the judgement of the lower court. The court had found Salman guilty under the Wildlife Protection Act, 1972.