The clause prevents Siemens from competing with the French company in some areas of nuclear plant business for eight years after ending the joint venture.
The European Commission said it had launched an investigation into whether the agreement between Areva and Siemens breached competition rules.
"The Commission will determine whether the non-compete clauses and the other contractual restrictions constitute a violation of the competition rules," it said in a statement.
"Siemens welcomes the announcement of the EU Commission. We have previously approached the Commission and had asked for a clarification of the matter," the conglomerate said, while Areva said it would cooperate fully with the Commission on the probe.
Two sources close to Siemens said the company filed a petition with the Commission in the autumn of 2009 contending the clause violated EU competition rules.
A company can ask for the Commission to take action if it believes a peer is violating the rules of the EU's single market.
Siemens tie-up with Russia's Rosatom
Areva and Siemens have been wrangling since early last year after Siemens announced it wanted to leave the Areva NP joint venture and sell its 35% stake to partner Areva.
The stake has a book value of two billion euros but analysts have said this could go up or down, depending on how the non-competition clause is resolved.
According to German daily Sueddeutsche Zeitung, Siemens estimates every new nuclear power plant built could generate some one billion euros in revenue.
An end to the dispute would pave the way for Siemens to proceed with a nuclear joint venture set up with Russia's Rosatom last year.
Talks on details of the tie-up - which would give Siemens a 49% stake in the venture - have been on hold since a French court blocked the deal until mediation over the Areva NP joint venture is completed.
However, analysts said it would not have a material impact on Siemens' share price.
"No matter how the whole thing ends, it will not have a significant impact on the share price. The Siemens joint venture with the Russians will be reflected as dividends because like the Areva joint venture, Siemens has the non-controlling part in the partnership," BHP-Bank analyst Jochen Klusman said.
(EurActiv with Reuters.)