Military prosecutors said they had referred all 13 to court on charges of forming a group to carry out "terrorist" acts and possessing banned weapons.
Security and judiciary sources said on Friday that investigations were under way to determine whether the suspects - seven Syrians, three Lebanese, one Saudi, one Jordanian with Lebanese nationality and one Palestinian - had carried out or were planning to launch attacks.
The arrests are believed to have taken place about two weeks ago, the sources said.
Al-Qaida has rarely launched attacks in Lebanon, although it has used allied factions to recruit scores of volunteers among Lebanese and Palestinian refugees who went to Iraq to fight.
Al-Qaida in Iraq has claimed responsibility for firing three Katyusha rockets from south Lebanon into northern Israel on 27 December.
There has been no independent confirmation that the group was behind that attack.
Israeli warplanes bombed a Palestinian guerrilla base just south of Beirut in retaliation for the strike.