The German deputy said the Commission's decision "enjoyed Parliament's full backing."
The aim of the ruling, he said, was to avoid a situation where "a few companies benefit from special rulings and the majority don't have a chance."
Apple has been accused of sheltering billions of pounds in profit in the Republic of Ireland tax-free, under a deal it reached with Irish authorities.
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Apple CEO Tim Cook branded the EU move as "total political crap" and the €12.8bn demand has also angered the US and worried Apple's peers.
The US Treasury Department has also warned the Commission about taking action against US companies over tax avoidance allegations.
The Apple furore has reignited the discussion of how much tax large companies should pay. Ferber, one of Parliament's leading experts on tax issues, warned that EU countries "need to understand" that attracting investment by granting tax deals is illegal under EU rules.
Ferber said, "Apple and other large multinationals have made it very easy for themselves. They say that we have these special tax rulings and we pay the taxes the state is asking for, so everything is legal. They are right from their point of view.
"This is why the Commission did not investigate Apple, IKEA, Fiat or Starbucks. The Commission investigated the Netherlands, Luxembourg and Ireland. Companies only have to pay their taxes the same way as every other company in these countries."
The EPP group deputy added, "This is what the member states have to understand. They can of course attract investment to their country, but they have to learn that doing so by granting tax deals is illegal under EU rules. As long as the national governments don't understand this, we can't complain about the companies."
He said international companies are said to only have one third of the tax burden of SMEs.
"If this is true, then this is something that we have to change. Those who generate profits in a certain country have to pay tax on that. It's not happening at the moment."
Despite fears about how Apple, which employs over 5000 people in Ireland, might respond to the EU ruling, Ferber still believes that Europe offers a stable business climate for foreign investment.
He said, "Europe is the world's most developed single market offering access to 500 million people. No other region in the world can deliver that kind of benefits. In addition the EU guarantees legal certainty. There are only a few markets as legally developed as the EU."
With the fallout from the Apple case still yet to be fully felt, Ferber says he "really appreciates" what European competition Commissioner Margrethe Vestager's work on the issue.
"She has the full support of the European Parliament from all political groups. This is something that we have to deliver to citizens. We can't have a situation where a few companies benefit from special rulings and the majority don't have a chance," he said.