The Metro system has awarded a $50.9 million contract for construction of the Shaw area subway station to the second-lowest bidder after a federal judge upheld its decision to reject the lowest bid, which did not meet minority business requirements.

The award was formally made last week to Mergentime Corp. of Flemington, N.J., and Perini Corp. of Framingham, Mass.

A joint venture of S.A. Healy Co. of McCook, Ill., and Vanessa General Builders Co. of Bridgeview, Ill., had bid $1.5 million less, but a transit authority hearing board determined that Vanessa, a black-owned firm, was not capable of performing 20 percent of the work, as provided by Metro's minority set-aside requirements.

U.S. District Court Judge Louis F. Oberdorfer ruled that Metro had acted properly in rejecting the Healy-Vanessa bid and in refusing to allow Healy to substitute other minority subcontractors after Vanessa had been disqualified.

Oberdorfer said Metro's inquiry showed that Vanessa could not post a construction bond and operated mainly as a "broker" for companies trying to comply with government rules on minority contracting. He said Vanessa's largest job in the past three years was worth $600,000, compared to the $10 million proposed for Metro.

The ruling "sends a message to industry that we are very concerned about our minority contracting program," said Frank R. Filiatreau, Metro's assistant general counsel. "We just don't want any bids that aren't going to comply."

Mergentime and Perini are white-owned but have promised that at least 20 percent of the Shaw work will be performed by minority contractors that Metro has certified.

The Shaw station, at Seventh Street NW between R and S streets, is part of the long-delayed Green Line, the only unopened route in the planned 103-mile Metro system. Officials said that with the contract award, the authority will be able to meet its schedule to open the station in 1990.

On July 30 the federal Urban Mass Transportation Administration also upheld Metro's decision to reject the Healy-Vanessa bid, declaring that the agency had a "rational basis" for its decision.

In his ruling Oberdorfer said that by rejecting the bid, Metro not only was complying with federal law but also was "discharging its public responsibility." An attorney for the Healy firm said the decision will not be appealed.