Logistics.com, an application service provider, helps shippers and transportation companies buy, sell, manage and optimise transportation services over land, air and sea.
Internet Capital Group, an e-business incubator with a 97% stake in the company, is backing Logistics.com.
ICG said that it expects to earn $12m from the sale of Logistics.com after it repays certain debts and other costs.
Eric Peters, senior vice-president for product strategy, marketing and alliances at Manhattan Associates, said the acquisition of Logistics.com would allow the company to expand its foothold in the supply chain market.
After the acquisition, Manhattan Associates anticipates hiring some of Logistics.com's 100 employees, Peters said. Logistics.com spokesman Evan Eggers said that most Logistics.com employees were likely to become Manhattan Associates employees.