Sosa, eighth on the career home run list, got 12.5 percent.
"If there was ever a ballot and a year to make a statement about what we didn't do as players - which is we didn't actively push to get the game clean - this is it," former Phillie Curt Schilling said on ESPN. "Perception in our world is absolutely reality. Everybody is linked to it. You either are a suspected user or you're somebody who didn't actively do anything to stop it. . . . And now this is part of the price that we're paying."
Bonds, Clemens, and Sosa were eligible for the first time and have up to 14 more years on the writers' ballot to gain baseball's highest honor.
"After what has been written and said over the last few years I'm not overly surprised," Clemens said in a statement he posted on Twitter.
Craig Biggio, 20th on the career list with 3,060 hits, topped the 37 candidates with 68.2 percent of the 569 ballots, 39 shy of election. Among other first-year eligibles, Phoenixville native Mike Piazza received 57.8 percent and Schilling 38.8.
Jack Morris led holdovers with 67.7 percent. He will make his final ballot appearance next year, when fellow pitchers Greg Maddux and Tom Glavine along with slugger Frank Thomas are eligible for the first time.
Two-time NL MVP Dale Murphy received 18.6 percent in his 15th and final appearance.
"It's a tough period for evaluation, that's what this chalks up to," Hall president Jeff Idelson said. "Honestly, I think that any group you put this to would have the same issues. ... There's always going to be discussion and concern about players who didn't get in, but at the end of the day it's a process, and again, a snapshot in time isn't one year, it's 15 with this exercise."
Bonds, baseball's only seven-time most valuable player, hit 762 home runs, including a record 73 in 2001.
"It is unimaginable that the best player to ever play the game would not be a unanimous first-ballot selection," said Jeff Borris of the Beverly Hills Sports Council, Bonds' longtime agent.
Since 1961, the only years the writers didn't elect a candidate were when Yogi Berra topped the 1971 vote by appearing on 67 percent of the ballots cast and when Phil Niekro headed the 1996 ballot at 68 percent. Both were chosen the following years when they achieved the 75 percent necessary for election.
The other BBWAA elections without a winner were in 1945, 1946, 1950, 1958, and 1960.
Commissioner Bud Selig, at the owners' meetings in Paradise Valley, Ariz., said: "This idea that this somehow diminishes the Hall of baseball is just ridiculous, in my opinion."
Players' union head Michael Weiner called the vote "unfortunate, if not sad."
"To ignore the historic accomplishments of Barry Bonds and Roger Clemens, for example, is hard to justify. Moreover, to penalize players exonerated in legal proceedings - and others never even implicated - is simply unfair. The Hall of Fame is supposed to be for the best players to have ever played the game. Several such players were denied access to the Hall today. Hopefully this will be rectified by future voting."