The Metro board voted yesterday to award a $50.9 million contract to two construction companies to build a subway station on the long-stalled Green Line in Washington's low-income Shaw area, after rejecting a lower bid by a group alleged to have violated minority-business requirements.

The station's construction is expected to be delayed, however, because of protests by the rejected bidder. The rejected group, which submitted a $49.4 million bid, has challenged Metro's actions in U.S. District Court here and has filed a protest with the federal Urban Mass Transportation Administration.

In another move, the Metro board awarded a $41.5 million contract to another construction company to build a Green Line station in Anacostia. Work on the station, near the Anacostia Freeway and Howard Road SE, is expected to begin in August.

The Anacostia contract was awarded to Kiewit Construction Co. of Omaha, which submitted the lowest of 10 bids. Metro officials said the company has complied with minority business rules, and there has been no controversy over the contract.

The Anacostia and Shaw stations currently are scheduled to open in 1990. Metro officials have warned, however, that any court order prohibiting work on the Shaw station may further delay the Green Line, the only unopened route in the planned 103-mile Metro system. The Shaw stop is to be at Seventh Street NW between R and S streets.

A federal review of the protest over the Shaw contract is likely to take about two months, according to federal officials. Judge Louis F. Oberdorfer has not indicated when he may rule in the dispute.

The Metro board voted to award the Shaw contract to a joint venture consisting of Mergentime Corp. of Flemington, N.J., and Perini Corp. of Framingham, Mass. Officials said the group had complied with minority-business rules, which require 20 percent of the work to be carried out by companies owned by minority persons.

The rejected bidder was a joint venture formed by S.A. Healy Co. of McCook, Ill., and Vanessa General Builders Inc., a black-owned company based in Bridgeview, Ill. Vanessa has been the focus of allegations labeling the firm a "sham" and a front for white-owned businesses.

After an investigation, Metro officials rejected the Healy-Vanessa bid, contending that the group had shown "a lack of good faith" in complying with minority-business rules. The companies have denied the allegations.

In other developments yesterday:

* Officials recommended what were described as relatively minor changes in bus service on 21 Metrobus routes in the District. The routes are 42, 50, 52, 54, 70, 92, A4, A5, B4, E2, E4, H2, H4, L2, L4, M12, M18, S1, S2, V3 and X8. Public hearings are scheduled for Sept. 4 and 5.

* The Metro board scheduled a public hearing Aug. 7 in Rockville on a proposal to increase parking fees from $1 to $2 a day at the crowded Metro lot at Grosvenor and to allow free parking temporarily at the underused lots at White Flint.

* Plans were announced for special bus and subway service on July 4, with fares set at 75 cents for the holiday.