The Nigerian defender has however introduced into the game with the home side already ahead through a Glenn Murray penalty.
Crystal Palace fell to a disappointing defeat as they were beaten 3-1 by rivals Crystal Palace.
Shortly after Shane Duffy was sent off, Brighton doubled their lead off a corner.
Murray returned to the starting line-up after being rested against Huddersfield and Andone's victor at the John Smith's Stadium may have made Hughton's decision tough to take.
Palace have been very good in their own end this season, conceding only 17 goals, the sixth fewest in the Premier League this season.
In his 300th Palace appearance, Zaha was up against the side he has scored more goals versus than any other.
Grace Millane: Backpacker's disappearance being treated as suspected murder
DI Beard confirmed that the man being questioned by police on Saturday was the same individual. Searches have also been carried out at the backpackers' accommodation where she was staying.
It was the second quickest by a substitute after Daniel Sturridge's goal versus West Ham United - a feat achieved after 24 seconds.
'Florin Andone has come in and got two goals in his first two starts, we are really pleased for him because he's put a lot of work, ' Hughton said at a press conference reported by the club. It was key for his first-half goal and kept Palace on their toes as the hosts sat back after the interval.
Brighton have now won six Premier League games this term and are placed 10th with 21 points in the EPL log.
"The pattern of the game is impossible to envisage - things happen and you have to deal with them".
Luka Milivojevic of Crystal Palace scores a penalty for his team's first goal. Brighton will take on Burnley at Turf Moor on the same day.
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