Outlining her decision, the judge said the couple's 250-square-metre (820 square foot) apartment could easily be turned into two separate living spaces with "minor adaptions".
After the work is carried out, the wife will live upstairs with four bedrooms and three bathrooms while her husband will have a downstairs unit with three bedrooms and two bathrooms.
The judge admitted there might be initial "suspicions" after the unusual decision, according to Spain's El País newspaper.
But she also argued the occasional awkward moment on the stairs was the "lesser of the two evils" given the "difficult economic panorama" facing the couple.
She also said the new living arrangements would mean the couple's two young daughters got to see both their father more often.
The father will now have to pay for the renovations, although it is his parents that own the disputed property.
His wife will also receive an allowance of €650 ($860) a month for one year — an amount awarded because her husband had convinced her to stay home and look after the children.
But the judge has asked the woman to review her request for €7,135 a month from the father of her children.
The Seville judge's decision to split a house down the middle is reminiscent of the 1989 comedy The War of the Roses.
In that film, a warring couple divide their family home by carefully measuring square metreage on the house's plans.