Jaffna High Court judge Manikkavasagar Ilancheliyan ordered the convicted soldiers to pay a compensation of Rs 500,000 to one victim and Rs 100,000 to the other woman raped in the northern Mullaitihivu district on June 6, 2010.
The women were raped a year after government forces claimed victory over separatist Tamil Tiger rebels and ended over three decade-long civil war, which killed at least 100,000 people.
The judge said that if the soldiers failed to pay compensation to the victims, they would have to undergo five more years in prison.
The judge lamented that the incident that happened after the end of the civil war in 2009 had shown that the military had failed the civilians.
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Sri Lankan army personnel have been accused by rights groups of using sexual violence on Tamil detainees even after the end of the separatist war. However, prosecutions of army personnel for sex crimes are rare.
The UNNHRC chief Zeid Ra'ad Al Hussein had said that Sri Lanka's judiciary and investigative processes had failed to deliver justice to victims of war crimes.