Much of the criticism has rightfully focused on Article 13, which would result in risky, preemptive, automatic filtering of content without necessary safeguards to protect creativity online.
Despite the amendments, some still view the laws as hindering freedom of expression online.
The reform amounts to a tussle over money between European content publishers and platforms such as Google and Facebook, which benefit from connecting viewers and that content, writes Politico (whose owners are lobbying for the directive).
The original proposal was rejected in July.
Music industry groups IFPI, IAO, Impala and Emma, which together represent producers, performers, independent music labels and European music managers, are demanding a change in the law.
After the vote, European Commission Vice-President for the digital single market Andrus Ansip and Commissioner for digital economy and society Mariya Gabriel also welcomed the outcome.
"At the same time, we aim to safeguard free speech and ensure that online platforms - including 7000 European online platforms - can develop new and innovative offers and business models".
Hurricane Florence track update on Thursday morning
Forecasters say Hurricane Florence is still a unsafe storm, despite its winds weakening as it moves closer to the U.S. The hurricane's surge could cover large swathes of the Carolina coast under as much as 11ft (3.3m) of seawater.
Article 11 is meant to give publishers and newspapers a way to make money when companies like Google link to their stories, while Article 13 requires platforms like YouTube and Facebook to scan uploaded content to stop the unlicensed sharing of copyrighted material. Requirements for platforms to filter all user uploaded content will likely result in a reduced user experience and the over-removal of legitimate content.
A final deal will be discussed with member states, before being put to a final vote in January 2019.
After that it will need to be implemented by individual European Union member states, who could very well vary significantly in how they choose to interpret the directive's text.
To be clear, the United Kingdom leaving the European Union will not protect United Kingdom businesses from these new requirements.
The directive is an optional implementation across the EU.
Nothing that happened yesterday has made me change my mind.