Defeated 2-1 in Juba in the reverse fixture last Wednesday, the East African minnows failed to turn things around against a much stronger Benin team.
While it was the visitors who started the better of the two sides, Benin had the first clear scoring opportunity with Genaro pulling off a fine double-save to deny Mickaël Poté on 9 minutes.
Squirrels’ skipper Stéphane Sessegnon drew another impressive save from the South Sudan ‘keeper in the 21st minute, but Genaro couldn’t do anything to stop the West Brom midfielder three minutes later.
The visitors came close to equalizing just before the half-an-hour mark, following a poor clearance from the Beninese defence, but it was the locals who ultimately doubled their lead, with David Djigla running down the left flank before squaring for an unmarked Poté at the near post on 38 minutes.
Omar Tchomogo’s men entered the break with their two-goal cushion, and could have piled more misery on their opponents on the restart when Sessegnon hit the woodwork following good work from Jodel Dossou.
However, the latter scored his side’s third goal with a low shot from inside the area in the 67th minute
Tong managed to pull one back for South Sudan five minutes from time, as substitute Abdel Fadel Suanon failed to restore Benin’s three-goal lead on 88 minutes.
But that was not over in Cotonou, with Sessegnon hammering a final nail in the visitors’ coffin in stoppage time.
Benin are now one point clear of Mali at the top of the table, with the Eagles having the opportunity to reclaim the leadership when they take on Equatorial Guinea in Malabo on Monday.