At half-time the match was exactly mirroring August’s Premier League fixture between the clubs at the Tottenham Hotspur Stadium, with Newcastle again leading 1-0 through a Joelinton goal.
However, Sissoko equalised early in the second half, scoring as his own player against his old team.
It looked like the pair were going to play out the first draw of the tournament and head to Golden Goal. But Atsu grabbed the victory in the 89th minute with a header from Jonjo Shelvey.
“I will have to change maybe my formation because he is very good at attacking," said Atsu.
"He has fast wingers and fast strikers, his midfield is very good, so I will have to be more compact even than this one."
Raheem Sterling (MCI) 5-4 Wilfried Zaha (CRY) | Report and highlights
Tom Grennan (MUN) 1-5 Trent Alexander-Arnold (LIV) | Report and highlights
Reece James (CHE) 0-8 Andre Gomes (EVE) | Report and highlights
Moussa Sissoko (TOT) 1-2 Christian Atsu (NEW)
The prize fund is being donated to the #PlayersTogether initiative, created by Premier League players as a collective way of generating funds for the National Health Service and distributing them where they are needed most.