Two officials confirmed the Stade Geoffrey-Guichard had been temporary cleared of all staff and spectators, who were allowed back into the ground after the all-clear was given around three hours before the 2100 (1900 GMT) kick-off.
Officials said the incident was down to an alarm being triggered by accident.
Portugal coach Fernando Santos said before the tournament got underway that the presence of three-time World Player of the Year Ronaldo made Portugal a potential target for terror attacks.
Ronaldo will attempt to become the first man to score in four different Euros against minnows Iceland, who are making their debut in a major tournament.