Selig said either he or a representative would attend the Giants' next few games "out of respect for the tradition of the game, the magnitude of the record and the fact that all citizens in this country are innocent until proven guilty".
Aaron was not in attendance. The player nicknamed Hammer is not following the chase in person.
"We as baseball players, especially as African-American ballplayers, have so much respect for Hank Aaron and all our fellow African-American athletes as well. They have paved the road for what we're doing now," Bonds said.
As has been the case at nearly every venue he has played since his drugs controversy began, Bonds' homer drew a mixed reaction from the crowd.
But Bonds was in a charitable mood after the match.
"I want to thank the fans. They have been outstanding," Bonds said.
"It's been a fun ride. I really appreciate the way San Diego handled it and the way their fans handled it."
Bonds walked his next three times at the plate and left the game in the eighth for a pinch-runner.
He raised his helmet with his left hand, then his right, and drew a standing ovation from many fans who chanted his name.
Bonds will not start on Sunday, saving his attempt to break the record until a series of home games starting on Monday.
Earlier in the day, Alex Rodriguez hit his 500th home run, and both men donated their helmets to the Hall of Fame.
The Yankee's Rodriguez is considered as the man most likely to break Bonds record once it is finalised.
The 32-year old is already ahead of Bonds pace at the same age.
The fan lucky enough to catch the Bonds ball, expected to fetch seven figures at auction, was 33-year-old Adam Hughes, who was whisked to a secure area so the specially marked ball could be authenticated.
Even with Bonds at 755, there is bound to be a split among fans over who is the real home run champ.
There will be some who always consider Babe Ruth as the greatest, while others will give that honor to Aaron, who was respected for his quiet dignity when he broke Ruth's record in 1974.