Parliament, meeting in a plenary session in Strasbourg, France, approved both measures by large majorities Tuesday.
The sulfur content bill aligns the EU legislation with the stricter standards for marine fuels agreed to in 2008 at the International Maritime Organization. It lowers the maximum permissible sulfur content of maritime fuels used in sensitive areas such as the Baltic Sea, the North Sea and the English Channel from 1.5 percent to 0.1 percent by 2015.
Other areas are targeted for an even bigger cut -- from 4.5 percent to 0.5 percent -- by 2020.
The energy efficiency legislation mandates renovations for public buildings as well as energy-saving schemes for utilities and energy audits for all big companies. Its goal is to cut energy consumption 20 percent, with envisioned savings of $65 billion per year.
The sulfur fuel-content mandate was passed despite strong opposition from Finnish business interests, especially the country's forest products and papermaking industries, which make heavy use of Baltic Sea shipping vessels to move products to export markets.
But EU officials say sulfur emissions from shipping contributes to air pollution in the form of sulfur dioxide and particulate matter, which harm human health and contribute to acidification.
The amended directive aims to force ships to use cleaner fuel in a bid to "address persistent air quality problems" in advance of a wider European Commission review of air policy scheduled to be taken up before 2013.
"While the new rules may pose challenges for the sectors concerned, the use of alternative abatement technologies, such as exhaust gas cleaning systems, as an alternative to using low sulfur fuels, will significantly reduce compliance costs and stimulate innovation and resource efficiency as a basis for the green economy," EU Environment Commissioner Janez Potocnik said.
Finland's government has budgeted $39 million to help shipowners retrofit vessels with the exhaust systems, known as wet scrubbers, which can cost up to $6.5 million each, YLE Finnish Radio reported.
Finnish Minister of Economic Affairs Jyri Hakamies said the government will also investigate ways to support exporters hit by increased costs.
Meanwhile, the approval of mandatory energy-saving measures will help stimulate green energy jobs, Claude Turmes, a member of the European Parliament for Luxembourg's Green Party, said in a statement.
"This essential legislation is not only crucial for achieving our energy security and climate goals -- it will also give a real boost to the economy and create jobs," Turmes said.
He predicted it will reduce the "sizeable and growing cost" of Europe's dependence on energy imports, estimated last year at $627 billion, or 3.9 percent of the European Union's gross domestic product.
The effects of improved energy efficiency will be particularly felt in countries hit by the European financial crisis, Turmes said.
The provisions include a requirement for EU member states to renovate 3 percent of the total floor area of "heated and/or cooled buildings owned and occupied by their central government."
They also mandate that energy companies achieve energy savings targets by 2020. The targets have been set at 1.5 percent of their yearly energy sales each year leading up to 2020.