The San Francisco slugger tied the record by slammnig a 1-1 pitch from Houston rookie Wilfredo Rodriguez to lead off the ninth inning.
The superstar left fielder had been pitched around by the San Diego Padres and Houston Astros since hitting his 69th homer on Saturday.
Houston pitchers had walked him three times Thursday night, but with the Giants already owning a 9-2 advantage going into the ninth, Rodriguez went after Bonds.
After being frustrated throughout the series, Bonds was ready to attack and he knew he had achieved baseball history the moment the ball left his bat.
He raised his arms in triumph before leaving the batter's box and he trotted to first base with his right arm raised skyward.
The crowd at Houston's Enron Field gave him a standing ovation as he celebrated his record-equaling home run.
Bonds has three games remaining in which to try to surpass McGwire and claim the record by himself. The Giants end the season with a three-game series beginning Friday night at home against the Los Angeles Dodgers.
"I'm really happy. I'm glad my family was here," Bonds said.
The blast traveled 454 feet and was caught by Charles Murphy, a Houston resident.
Until hitting the homer, Bonds had been walked eight times in the three-game series, collecting two hits in five at bats. He broke Babe Ruth's single-season walks record of 170 Wednesday night.
Dozens of fans hung posters and carried placards that implored the Astros to pitch to Bonds so they would have the chance to witness history.
All season, Bonds had matched or bettered McGwire's record pace of 1998, when the St. Louis slugger shattered Roger Maris' 1961 record of 61.
Bonds' first chance to break the record will come Friday night against righthander Chan Ho Park.
The homer was the 564th of Bonds' career, moving him past Hall of Famer Reggie Jackson into seventh place on the all-time list.
Bonds has passed 10 players this season, all Hall of Famers or certain future inductees.
Unlike just about every Astros pitcher before him, Rodriguez seemed intent on challenging Bonds. The 22-year-old began by throwing a high fastball past Bonds before leaving one out of the strike zone.
Rodriguez's next pitch moved him into forgettable company with Tom Zachary, Tracy Stallard and Steve Trachsel.
Zachary gave up Babe Ruth's 60th homer in 1927, Stallard allowed Maris' 61st in 1961 and Trachsel surrendered McGwire's 62nd in 1998.