The Finance Secretary announced a £20 million fund, for this year only, to help offset the impact of the widely criticised housing benefit cuts.
But Scottish Labour, the STUC and charities accused him of doing too little to help tenants struggling to pay rent.
He was left facing claims he had left tenants "on the hook" as part of an ongoing political attack on UK Government welfare reforms.
The row came as he unveiled a £35.5 billion budget for 2014/15 and outlined indicative spending plans for the following year.
Mr Swinney found extra cash for affordable housing and pledged to secure £8bn of infrastructure investment over the next two years. He also announced £24m for a National Performance Centre for Sport, to help ensure a legacy from the Commonwealth Games.
He stressed that the Government's universal entitlements, such as free prescriptions, would be protected.