Nkunku's maiden goal for France, almost 10 months after his last cap, helped France to six points from three games, one behind Italy who were held to a 2-2 home draw by Belgium.
The Chelsea forward struck midway through the first half after Omri Gandelman had cancelled out Eduardo Camavinga's early opener before Matteo Guendouzi and Bradley Barcola sealed the win in the closing stages.
France were without regular captain Kylian Mbappe, who skipped the double header with Israel and Belgium, away on Monday, while fit to play with Real Madrid.
"It's always good to win. The atmosphere around the squad is not exactly pleasant," coach Didier Deschamps said, referring to the criticism Mbappe faced for missing the games and a poor performance against Italy last month.
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