Democrats broke through a Republican filibuster on the bill on Tuesday, as the chamber voted to end debate on a substitute amendment.
Republicans disagreed with the $30 billion lending fund, calling it a "government bailout."
Groups representing community banks said the fund could spur $300 billion in loans to small businesses.
Lawmakers also were at odds over how to move forward on a 1099 filing requirement in the healthcare law that affects small businesses.
Two amendments, one from each party, failed to garner enough support to make changes to the filing requirement, which requires business to provide 1099 tax forms on $600 on goods and services they purchase.
Republicans have moved to repeal the provision, and Sen. Mike JohannsMike JohannsLobbying World To buy a Swiss company, ChemChina must pass through Washington Republican senator vows to block nominees over ObamaCare co-ops MORE (R-Neb.) said on Wednesday he plans to continue the campaign to remove it from the law.
Several Democrats have offered a variety of proposals that range from repealing the provision to raising the limits from $600 to $5,000 on goods and services they purchase and were hoping to take action before Congress recesses for the midterm elections.
The provision is expected to raise about $17 billion to pay for the healthcare law, and lawmakers are looking for ways to pay for the measure, including using stimulus funds.