"I don't see what I have done," he said from the defendant’s cage. "I expressed my opinion...the intention was not anything like these [charges]."
Nabil, a former student at Egypt's Al-Azhar University, has often denounced Islamic authorities and criticised Mubarak on his Arabic-language blog.
The judge, Ayman al-Akazi, said he would announce his verdict on February 22. The trial began in Alexandria on January 18.
Nabil's detention has caused outrage among human rights groups.
On Thursday Amnesty International called for Nabil's "immediate and unconditional release."
Nabil "is being prosecuted on account of the peaceful expression of his views about Islam and the al-Azhar religious authorities," Malcolm Smart, the group's Washington-based Middle East and North Africa Program director, said in a statement.
Nabil was thrown out of Al-Azhar University because of his writings and the institution pressed authorities to put him on trial.
Prosecution arguments in Thursday's session were given by a team of Islamist lawyers who volunteered to serve as the "representatives of the people," an arrangement allowed under Egyptian law.
The government's state prosecutors, who drew up the legal case against Nabil, were not present.
Nabil "has hurt every Muslim across the world," argued one of the lawyers, Mohammed Dawoud. He urged the judge to hand Karim the maximum punishment
Dawoud called Nabil an "apostate" sparking shouts from the defence lawyers and a heated exchange until the judge demanded order.
Nabil's defence lawyers avoided making a case for Nabil's right to write about Islam, instead focusing on technical aspects and arguing that the prosecution's written case against Nabil was incomplete.
Seif el-Islam, the chief defence lawyer said the court should appoint an expert to examine the evidence. The defense has raised questions whether the Internet server was based in Egypt and therefore whether a crime was committed in Egypt.
Fellow defence lawyer Mohsen Bahnasawi argued that crimes related to the Internet were new in Egypt and that the penal code did not cover them.
Dawoud asked the judge to add a fourth charge of "insulting a sect," punishable with another five years in prison. The judge did not immediately respond.
"I want him [Nabil] to get the toughest punishment," Dawoud told The Associated Press. "I am on a jihad here ... If we leave the likes of him without punishment, it will be like a fire that consumes everything."
Egyptian security forces arrested a number of bloggers last year - usually in connection with their links to protests by democratic reform activists.
All have been released, except Nabil, who was the only one to deal with the sensitive topic of religion in his writings.
In his blog, where he uses the name Kareem Amer, Nabil was a fierce critic of conservative Muslims and in particularly of al-Azhar, which he denounced as "the university of terrorism".