The result highlighted Guardiola as winning five Carabao Cup titles and becoming the first manager in the history of the tournament to achieve the feat.
The Gunners secured a crucial win towards the end of the game, scoring their two goals in the 89th and 97th minutes.
Chelsea moved to fifth on the table with 48 points.
The Gunners restored their lead in the 66th minute through Jurrien Timber who headed home a well-placed corner kick by Declan Rice.
The game was a must-win for Arsenal in the battle for league title this season.
Bukayo Saka put Arsenal ahead only five minutes into the encounter.
Arsenal dropped crucial points in the battle for the Premier League title after they were held to a 1-1 draw by Brentford at the Gtech Community Stadium on Thursday night.
Arsenal fans will now focus their attention on the game between Liverpool and second-placed Manchester City on Sunday.
The Unify League is a breakaway league proposed in 2021 to rival the traditional UEFA Champions League.
Arsenal will face Man City in Wembley for the Carabao Cup final.
