The 16 men arrived at an army checkpoint in the mountainous Jurud Arsal region of eastern Lebanon in four Red Cross vehicles, live footage showed.
Lebanon's General Security service confirmed that the men -- three soldiers and 13 policemen -- had been turned over to authorities.
The 16 were among 30 Lebanese soldiers and police kidnapped in August 2014 when Al-Qaeda affiliate Al-Nusra Front and the Islamic State group briefly overran the Lebanese border town of Arsal.
Al-Nusra subsequently executed two of its hostages, including Mohammed Hammiya, whose body was turned over to Lebanese authorities earlier on Tuesday in the first stage of the swap deal.
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IS also beheaded two of its hostages, and a fifth died of wounds he sustained during the fighting in Arsal.
The fate of the other 25 servicemen has been an ongoing crisis for the Lebanese state, which has entered negotiations multiple times to try to secure their release.
Nine detainees remain in IS custody, though it is unclear whether negotiations are ongoing for their release.
But several said their joy was "incomplete" without the release of the nine men still held by IS.