The agency also lowered the ratings for: farm lenders; long-term U.S. government-backed debt issued by 32 banks and credit unions; and three major clearinghouses, which are used to execute trades of stocks, bonds and options.
All the downgrades were from AAA to AA+, reflecting the same downgrade S&P made of long-term U.S. government debt on Friday.
S&P said the agencies and banks all have debt that is exposed to economic volatility and a further downgrade of long-term U.S. debt. Their creditworthiness hinges on the U.S. government's ability to pay its own creditors.
Stocks plunged further after the downgrades. The Dow Jones industrial average fell more than 300 points, or 2.8 percent. The S&P 500 stock index tumbled 3.4 percent. Investors seeking safety drove gold prices up and Treasury yields down.
Monday's downgrades of the mortgage giants Fannie and Freddie reflected their "direct reliance" on the U.S. government, S&P said.
Fannie and Freddie own or guarantee about half of all U.S. mortgages, or nearly 31 million home loans worth more than $5 trillion. As part of a nationalized system, they account for nearly all new mortgage loans. Their downgrade might force anyone looking to buy a home to pay higher mortgage rates.
Officials at Standard & Poor's say they will also indicate shortly how local and state governments will be affected by their decision to lower the long-term U.S. debt.
S&P on Friday said it downgraded U.S. debt for the first time in history because the credit rating agency lacks confidence that political leaders will make the choices needed to avert a long-term fiscal crisis.
The downgrade of long-term debt issued by the U.S. government affects the banking and lending industries because many interest rates are pegged to the yields on Treasury securities. In addition, many companies use the securities as collateral that they would surrender if their bets lost value.
The lower credit rating for long-term U.S. debt means that it might be considered less valuable for those purposes. It might become more costly for companies to borrow or trade.
Some analysts said the downgrades were unlikely to have much effect on the companies named by S&P or the broader markets. They noted that Treasury yields remain low and the dollar is getting stronger -- signs that the world still sees the U.S. as a safe harbor in volatile economic times.
The downgrades "are as meaningless as the original action," said Daniel Alpert, managing partner at the investment bank Westwood Capital LLC in New York. He said that investors are rushing into Treasurys, and that they will do the same for "anything backed by the full faith and credit" of the U.S. government. That includes debt issued by Fannie and Freddie and bank debt that was guaranteed by regulators to ease lending after the 2008 financial crisis.
The yield on the benchmark 10-year Treasury note fell to 2.38 percent from 2.57 percent late Friday. Analysts say traders are shifting out of bonds and European banks are snapping up U.S. debt to steel themselves for a regional financial crisis.
S&P Managing Director John Chambers said that the credit rating agency believes the dollar won't be weakened "under any plausible scenario." He said it will remain the dominant international currency, and that will reduce interest rates for governments and the private sector.
Ten of the country's 12 Federal Home Loan Banks also were downgraded from AAA to AA+. The banks of Chicago and Seattle had already been downgraded earlier to AA+.
A spokesman for Freddie Mac declined to comment on the move.