The three belonged to the al-Almi faction of the Harkat-ul-Mujahideen, a group that is also blamed for masterminding a suicide attack outside the US consulate in Karachi last year, that left 12 people dead.
Judge Aale Maqbool Rizvi of an "anti-terrorism" court said the three men were found guilty of plotting to kill Musharraf in April last year on his way to address a public rally in the port city of Karachi.
The judge acquitted two other suspects citing lack of evidence.
The three, Muhammad Imran, Muhammad Hanif and Muhammad Ashraf parked a vehicle packed with explosives along a route the president was to take. Their plan failed when the remote-controlled detonator did not work.
Imran, who was described by the police as the ring-leader of the group, said he was innocent.
"All the cases against us are baseless," he said.
"We are being held in jail because the government wants to please Americans," he said as he stood in the courtroom inside the Karachi Central Jail.
Imran and Hanif were already given death sentences in April for the US consulate bombing.