The duo escaped after the train stopped when one of the passengers pulled the emergency chain, Railway police said.
Acting swiftly, local police, which launched a manhunt, took into custody the two youths, said to be belonging to a neighbouring state, they said.
The incident occurred on board Thiruvananthapuram-New Delhi Kerala Express as it reached between Kuruppanthara and Kothanallur, about 20 km from here.
The assailants boarded the train when it halted for signal near here and started beating up the couple with bare hands.
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Mohammed Nisar, whose vision is partially affected, and his wife Hayarunnisa suffered injuries and the latter fell unconscious in the attack.
Both have been admitted to a nearby private hospital where the woman was responding to treatment, police said.
Hailing from Kallambalam in Thiruvananthapuram, the couple were travelling to Piravom Road, a place near here, along with their child in the coach reserved for disabled passengers, police said.
A Railway police official said Kaduthuruthy police have recovered lost valuables from the youths.