Police armed with truncheon, shields and water hose faced the activists who were opposing a looming pact that will increase the American military presence in the Philippines.
The activists waved flags saying "Obama, not welcome" near the heavily fortified embassy compound and slipped past the police, sparking a brief scuffle.
A police officer was punched in the face but no arrests were made.
Obama will arrive in Manila on Monday for an overnight stop after visiting Japan, South Korea and Malaysia. He is expected to reassure allied nations enmeshed in long-running territorial disputes with an increasingly assertive China.
The accord will allow more US troops, aircraft and ships to be temporarily stationed in selected Philippine military camps as a counterweight to China and as a standby disaster-response force.
About 500 American soldiers have been based in the southern Philippines since 2002 to provide anti-terrorism training and intelligence to Filipino troops battling al-Qaida-linked militants.