The first bomb exploded in Baghdad's Sadr City while the second went off in the al-Kamaliya neighbourhood. Both are predominantly Shia areas.
The blasts were the latest in a string of attacks against the pilgrims in the past two weeks.
On Friday, 42 pilgrims on their way to Karbala were killed in a suicide attack. An attempted suicide bombing also took place on Saturday in the same area.
A day earlier, eight people were killed by a roadside bomb near the Imam Hussein mosque in Karbala.
Defying threats
Despite the threat of violence, thousands of Shia pilgrims have converged under high security in Karbala to mark the last day of Ashura, a 40-day mourning period for Shia Muslims.
Iraqi officials said millions of people have visited the city in the last week for the ritual in which Shias mourn Hussein, Prophet Mohammad's grandson.
The local police chief said that at least 30,000 police were deployed around the city to prevent further attacks.
Policewomen have been searching female pilgrims following an attack by a female suicide bomber.
Since the invasion of Iraq by US and British-led forces in 2003, Shia pilgrims to Karbala have frequently been attacked.