The 27-year-old fired a rebound into the net to make it 1-1 in the penultimate matchday fixture but it was the away side who had the last laugh at St. James Park.
It was his first Premier League goal in 40 outings and his maiden strike since netting against West Ham United in December 2017.
Liverpool were the first to score as Virgil van Dijk headed home Trent Alexander-Arnold's corner on 13 minutes.
Atsu drew parity for Newcastle seven minutes later, slamming home a rebound after Alexander-Arnold blocked Salomon Rondon's goal-bound shot on the line.
Alexander-Arnold was again involved in the third goal of the game, this time assisting Mohamed Salah to put Liverpool 2-1 up.
Nine minutes after recess, Rondon levelled the score for Newcastle once again, smashing a first-time shot into the net after the visitors failed to clear a corner.
It looked like the spoils were going to be shared until 73rd-minute substitute Divock Origi scored in the 86th minute to ensure a 3-2 triumph for Liverpool.
The three points temporarily puts The Reds two points clear at the top of the table while Newcastle sit in 14th position.
Atsu, who has made 27 league appearances involving 14 starts so far this season, is expected to maintain his starting spot in The Magpies' last match of the season against relegated Fulham on May 12.
He started two games in a row for the first time since February, Atsu's starting spot on Saturday was down to the absence of first-choice left winger Miguel Almiron, who is out injured.