Lee Bonis opened the scoring for Tiernan Lynch’s side on 50 minutes before goals from Sean Moore (59) and Rory Hale (75) turned the tie on its head and ensured the north Belfast outfit would take all three points.
Larne remain top of the standings thanks to a goal difference of plus 24 compared to Cliftonville’s plus 11.
Speaking to the club’s media director Ian Cahoon after the match, Lynch said: “A really disappointing game. I thought for long periods we were very good. We showed great fight, great courage, great determination. We played some really good football and created some really good chances.
"I think we got punished in our box on two occassions and that was the difference.
"We have to make sure that we stay in this pack and once you stay in the pack, you see where it takes you.”
Next up for Larne is a fifth round Irish Cup clash with Crumlin United at Inver Park on Saturday (3pm).
Larne’s east Antrim neighbours Carrick Rangers also started 2023 with defeat as they fell to a 3-0 loss at home to Crusaders.
Paul Heatley opened the scoring for the visitors on 10 minutes before Jordan Forsythe found the net to make it 2-0 shortly before the break.
Forsythe scored his second and his team’s third on 50 minutes and Stephen Baxter’s side held on for the win.
The result keeps Stuart King’s side ninth in the table on 23 points.
Carrick welcome Mid and East Antrim rivals Ballymena United to Taylor’s Avenue on Saturday in the Irish Cup (3pm).
Meanwhile, Ballyclare Comrades left it late to get all three points on the road at Warrenpoint in the Lough 41 NIFL Championship on Monday.
Owen McConville found the net on 89 minutes, getting his head on a Gary Donnelly corner.
Stephen Small’s charges sit sixth in the table on 29 points.
The Comrades welcome Dollingstown to Dixon Park in the Irish Cup on Saturday (3pm).