De Jong struck in the 55th minute with a shot from near the penalty spot after a long cross by Marcos Acuña from the left flank.
In the other group match, Chelsea won 4-0 at Krasnodar. Sevilla and Chelsea had drawn 0-0 in their opener. They lead the group with four points each, with Rennes and Krasnodar tied with one point each.
"We are happy with the three points."
On Jules Kounde, he added: "It was a matter of whether sooner or later we got it right and fortunately it happened."