A Rwandan official confirmed the deaths in the frontier town of Gisenyi and said a second shell had landed inside Rwanda near a border crossing, seriously wounding one person.
Last week, a 3000-strong UN intervention brigade with a mandate to neutralise armed groups launched an operation in eastern Congo against a rebel group widely believed to be backed by Rwanda.
Eyewitness Nizeyimana Hamis said of yesterday's strike: "The bomb killed two people, a woman and a baby."
A Rwandan official accused the Congolese army of firing the shells. Rwanda denies backing the so-called M23 rebellion but fears are growing the violence inside Congo could spill across borders.
A diplomat in the Great Lakes region said it was clear the rebels had received support from Rwanda to help counter the UN force's aerial and ground assault over the past week.
A UN peacekeeper from Tanzania was killed and three others were wounded on Wednesday in an operation to drive back M23 rebels from Goma in eastern Congo,