However, prosecutors told the court that the Rohingya were angered when a female asylum seeker was sexually harassed by the fishermen.
Lawyers for the 14 Rohingya said they were also considering filing an appeal.
"They had not planned the violence," said attorney Mahmud Irsyad Lubis. "It happened in an instant."
The Rohingya, who have been jailed since April, are expected to be freed from prison next month.
In July, the same court acquitted three Rohingya teenagers due to a lack of evidence of involvement in the violence.
Boatloads of Rohingya have been arriving on Indonesia's shores following a wave of religious violence in Myanmar, where they are considered illegal settlers from neighboring Bangladesh. Hundreds have been killed and more than 100,000 left homeless in clashes between Rohingya and ethnic Rakhine Buddhists.
The tensions have tested Myanmar's reformist government as it attempts to institute political and economic liberalization after nearly half a century of harsh military rule.