The main mechanism the EU Commission has to enforce binding rules is called the “infringement procedure”. It starts with a formal letter laying out why the Commission thinks a country doesn't apply EU law correctly and proceeding through several steps to a ruling by the EU Court of Justice (EUCJ). If the EUCJ agrees with the Commission and a member state doesn't alter its practices, the Commission can drag them in front the court again (it's called “manquement sur manquement” in the lingo of the court), which can then impose significant financial penalties.
Whether or not the Commission actively enforces a particular rule sometimes depends on political considerations but its powers are very extensive. There are usually 6 infringement packages a year, the last one in February 2021. If you peruse the press release, you will see the Commission is not shy about using this power and covers a lot of ground. It does however occasionally overreach and is not always successful in front of the Court. When it is, member states eventually comply, with very few exceptions.
The problem in this case is that those minimum tax rates are not EU rules at all. The threshold you are referring to was agreed by the G7. G7 decisions are inherently weaker, mere statement of intention rather than a firm commitment, let alone a binding rule. EU institutions are not in the business of enforcing non-EU rules.
On the other hand, if something is not part of EU law, there is little the EU can do to “force” its member states to do anything. Elaborating new rules like that requires a broad consensus in all three main EU institutions including the EU Council, which represents member states. Depending on the exact subject matter, a single member state has a lot of means to block decisions. If several of them have an interest in a lack of harmonization, they can stall forever.
In fact, outside of VAT, there is still very little EU harmonization of tax law. The differences between EU countries are still very big and there are many member states benefiting from all the quirks in tax law that absolutely do not want to let the EU regulate it, as any EU rule would have real teeth. This is so sensitive that the treaties themselves restrict what the EU can do regarding taxes, while ensuring that any rule must be agreed unanimously. That's also the reason why most of the recent push for more international rules in this area has come from the OECD, the G7, or even unilaterally from individual countries and not from the EU.