The energy ministry will now be headed by al-Zubeir Ahmed al-Hassan, the former finance minister.
The energy and finance positions are important in Sudan due to the more than 500,000 barrels of oil the country produces per day.
A Sudanese analyst who preferred not to be named said the reshuffle was just "pushing papers".
"The key people are still in key positions."
But Mardi's removal was a step forward to improve Sudan's image abroad, he said.
Ibrahim Ahmed Omer was appointed minister for science and technology.
A senior figure in President Omar Hassan al-Bashir's National Congress Party, Omer came out of retirement to advise Bashir on media matters.
Kassala Ibrahim Mahmoud Hamad, a former governor, was made minister of interior. He replaces al-Zubayr Bashir Taha, who was moved to the agriculture and forestry portfolio.