Mutharika, the brother of former president Bingu wa Mutharika, took 36.4 percent of the votes cast against Banda’s 20.2 percent, the electoral commission said.
The results were announced minutes after the high court refused a last-ditch attempt to block their release and allow time for a recount.
Electoral commission chief Maxon Mbendera declared Mutharika “president-elect” after last week’s vote, which Banda said was marred by “serious irregularities” and “null and void”.
The results showed that Banda was beaten into third place by Lazarus Chakwera of the Malawi Congress Party (MCP), who garnered 27.8 percent of the vote.
Party spokeswoman Jessie Kabwila told AFP the MCP, which had made the bid for a recount, would challenge the results in court.
“We are disappointed because this is not a credible election. We will fight through legal means…we are not taking this lying down.”
Mutharika is set to take the reins of the impoverished southern African country under the shadow of a treason charge.
The 74-year-old brother of former president Bingu wa Mutharika is accused of attempting to conceal his brother’s death in office two years ago in an attempt to prevent Banda – then vice-president – from assuming power.
Banda prevailed and took office as decreed by the constitution, booting the former foreign minister out of the administration.
Mutharika, a law professor and former cabinet minister, faces additional counts of inciting a mutiny and conspiracy to commit a felony, along with other officials.
The trial is still pending, but analysts say it is likely the case will be set aside as Malawi’s presidents enjoy immunity from prosecution as long as they are in office.
There is speculation that once Mutharika is in power he could turn the tables on Banda and have her charged with corruption over a $30 million graft scandal dubbed “Cashgate”.
Banda has claimed the credit for uncovering the fraud, which saw aid money siphoned into top government officials’ pockets. But critics, including Mutharika, say the funds went into her party’s election war-chest.