The unprecedented cross-border battles, which claimed the lives of two Syrian refugees and a Lebanese reporter, came just hours before a ceasefire deadline came into force.
The Turkish government, which has already threatened to take military action to protect its border, summoned Syria's envoy to Ankara to demand an official explanation.
According to Turkish officials, Syrian troops pursued rebels across the border following an attack on a checkpoint that killed six soldiers. Two Syrian nationals, described as civilian, were subsequently shot dead as they tried to escape to the nearby Killis refugee camp.
It was unclear whether the two victims had already crossed the frontier but five more people – including a Turkish policeman – were later shot and wounded, this time indisputably on Turkish soil.