Policymakers hope the new rules will plug failings in the existing legislation, identified in the recent financial crisis, and bring the regulation up-to-date with technological developments.
Algorithmic trading, for example, has been credited with causing the 2010 "flash crash," after high-frequency traders started aggressively selling. At that point, more than 60 percent of U.S. equity trades were accounted for by HFT, according to Bloomberg. The industry has become less profitable since then.
The negotiators agreed to push the organized trading of financial instruments onto regulated trading platforms, to end the so-called "dark trading" taking place away from regulated markets like stock exchanges.
The measures are expected to implemented by the end of 2016.
(Read more: Europeans struggle to set derivatives rules)
Michel Barnier, European Commissioner for Internal Market and Services, welcomed the deal – but said he would have preferred a "more ambitious" implementation period.
"These new rules will improve the way capital markets function to the benefit of the real economy," he said in a statement. "They are a key step towards establishing a safer, more open and more responsible financial system and restoring investor confidence in the wake of the financial crisis.
Arlene McCarthy, a British Member of the European Parliament from the Labour Party, said the regulation of high-frequency trading would "slow down the pace of trading, increase transparency and ensure prices reflect current market."
And with regards to the curbing of commodities speculation, she added: "For the first time, the EU will regulate commodities to tackle food speculation. High and volatile food prices have a devastating impact on poor and food dependent countries."
The rules, which will apply to investment firms and market operators, must be formally approved by European Parliament and EU-member governments before taking effect.
The British Bankers' Association, which represents the banking and financial services sectors in the U.K., said it "remained concerned about the impact of the new rules on the real economy by limiting market liquidity and hurting the competitiveness of European firms."