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A last-gasp goal by substitute Yaw Alexander from a Gladon Awako flick on, handed the champions the winner in injury time.
Steve Pollack's side conceded the opening goal when Fuseini Zuberu put the visitors in front after 37 minutes to register his second goal in the league.
Liberty's Isaac Sakyi was the first player to pick the yellow card when he was booked by referee Slyvester Adzoku in the 5th minute.
Chelsea's Emmanuel Clottey was also booked in the 42nd minute.
The home team soon pegged back Liberty from the spot after Yakubu Issah had fouled a Chelsea player in the box. Yakubu was booked for the challenge.
Captain Abdul Basit beat Akwesi Acheampong from the spot to draw his side level.
The game appeared to be heading for a draw when Alexander scored the winner from a tap-in.