The proposals initially attracted anger from defence solicitors who also opposed moves to make them collect the money instead of the Scottish Legal Aid Board.
Following talks with the Law Society, Justice Secretary Kenny MacAskill agreed to raise the contribution level from the proposed £68 to £82.
The change was endorsed by opposition parties during the passage of the Scottish Civil Justice Council and Criminal Legal Assistance Bill which reached its third and final stage at Holyrood.
Labour voted with the SNP on the new income limit despite concerns that the overall Bill remains "bad".
Malcolm Chisholm, Labour MSP for Edinburgh Northern and Leith, said the legislation is driven entirely by finance.
"The cabinet secretary has been forced to modify a very bad Bill so it ends up simply as a bad Bill," he said. "That doesn't alter the fact that it still is bad."
Tory MSP Annabel Goldie offered her support and said: "I'm glad that the cabinet secretary has yielded to his metaphorical beating over the head and improved what was a poor situation and made it somewhat better."
Mr MacAskill told Parliament: "These amendments reflect concerns expressed by members of the Law Society of Scotland that the original threshold of £68 might compromise access to justice."
MSPs also rejected two similar amendments by Labour and the Conservatives which sought to provide refunds of legal aid fees for people who have been acquitted.
The amendment by Labour MSP Graeme Pearson would have given the courts the discretion to provide a refund if it is "in the interests of justice".
This was rejected following a warning by Mr MacAskill that it could lead the public to doubt the innocence of those who are acquitted but have their refund rejected.
Mr MacAskill also questioned the ethics of giving a refund to those people whose trial was abandoned in circumstances such as the intimidation of witnesses.
"There are many circumstances where a case can conclude without a conviction," he said.
"For example, it may be deserted because of evidence coming to light during a trial; where a case is dropped because a witness failed to attend, perhaps because they were intimidated or frightened by the prospect of giving evidence. The accused person would receive a refund? Are these the circumstances envisaged by the amendment?"
An amendment to force the Scottish Government to review the legislation every three years was also rejected after Mr MacAskill gave a commitment to conduct a review in that timescale, and dismissed the requirement to enshrine this commitment in legislation.
Mr MacAskill said later that the changes would "deliver vital savings to ensure legal aid can be targeted at those who need it most"
He told MSPs: "Contributions to criminal legal aid will allow us to continue to target legal aid at those who need it most by asking those who can afford it to pay towards the cost of their defence.
"To be clear, no one is being asked to pay for the full cost of their defence. If they can do that, they would not be eligible for legal assistance. We are suggesting that where someone can afford to contribute towards the costs, they should be asked to do so."
Some defence solicitors are unhappy about the legislation which will see them have to collect legal aid contributions, he acknowledged.
"It is unlikely to have escaped anyone's notice that some in the profession are unhappy with the proposals. I appreciate many firms feel collecting some of these contributions is a burden placed on them at a difficult time. While I accept that concern, I don't think it is an unreasonable or unfair expectation.
"We are now dealing with a legal aid bill for 2011-12 which was the second highest on record. It will not reduce without action."
Mr MacAskill said "difficult decisions still need to be made" but that his "key priority" is maintaining access to justice.
But Labour's Lewis Macdonald said that the Scottish Government has "ignored the views of others" and is pushing through legislation which is "not fit for purpose".
He welcomed the "late and reluctant" changes made by the Government, including raising the threshold for people to pay a contribution towards the cost of their defence.
But Mr Macdonald said: "People with disposable incomes of £82 a week are still on very low incomes, which is why the new system will need to be carefully monitored if those people are to maintain fair and reasonable access to justice."
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