From 2014 under the new regulation, car manufacturers will have to reach a target of 175g of emissions per kilometre for 70% of their vehicles, rising to 100% of their fleet by 2017.
This would represent a cautious 14% emissions cut, at a time when Renault's Master van and Mercedes' Sprinter van have made efficiency gains of 15% and 13% respectively.
By 2020, failure to reach a target of 147g emissions per kilometre will then be met with fines of up to €95 per vehicle for every gram over the limit.
A tougher target of 135 grams per kilometre by 2020 had originally been proposed.
"This figure reflects a less ambitious compromise than many MEPs had wanted, but in line with the agreement reached [between member states]," the Parliament said in a statement.
EU Climate Commissioner Connie Hedegaard welcomed the vote, which she said would bring significant fuel savings for van users.
"It also gives vehicle manufacturers greater certainty about the emission targets they need to reach," she said. "At the same time it will contribute to cleaner air and to achieve our climate targets."
The European Automobile Manufacturers Association also hailed the new law, which it said "sets extremely challenging targets, in particular for the long term".
Bonuses and penalties
Under the deal, vans that emit less than 50g CO2/km will earn automakers "supercredits" for meeting their C02 reduction targets. Vans meeting these emission limits would count as 3.5 vehicles towards the average to be reached in 2014-2015, 2.5 in 2016 and 1.5 in 2017, the last year of the scheme.
On the other hand, each new van over the agreed limits will be subject to penalties rising to €95 per gram from 2019, the Parliament said.
The bill was sponsored by Martin Callanan MEP, leader of the UK Conservative MEPs, who as the Parliament's rapporteur was able to reach agreement with the EU Council of Ministers at first reading.
This means that the bill will face no further obstacles to implementation.
Callanan described the legislation as a "difficult balancing act" between the needs of the environment and car manufacturers.