With the San Francisco slugger leading off the fifth inning, Springer's first pitch sailed behind Bonds' back, drawing a warning from plate umpire Joe West.
The next four pitches all came inside, including one that hit Bonds' bat handle on the third delivery for strike one. The fifth pitch hit Bonds as he turned to protect himself.
That's when Springer and manager Phil Garner got ejected -- and the Houston crowd gave Springer a standing ovation.
Bonds was unhurt and trotted down the first-base line and later scored on Jose Vizcaino's RBI single to give the Giants a 12-3 lead.
The 41-year-old Bonds had already singled twice and driven in a run in San Francisco's five-run first. He also flied out at the warning track in right.
Bonds was playing for the eighth straight game in as many days in his pursuit of Babe Ruth's 714 home runs for second place on the career list.
Springer relieved Houston starter Wandy Rodriguez, who lasted only 3 2/3 innings.