Defending champions Germany have been eliminated from the World Cup at the group stage following defeat by South Korea, in one of the biggest shocks in the competition's history.
First, it's important to note that this is a news headline written in a journalistic style.
This is not how a native speaker might normally construct a standard English sentence. News headlines often remove or rearrange words to squeeze more information into a small space.
The following version adds some of the implied/elided words back in:
[The] defending [World Cup] champions, Germany, have been eliminated from the [current] World Cup [during] the [first] stage [of the tournament], following ['a', or 'their'] defeat by South Korea. [Germany's early elimination from the tournament] is one of the biggest [unexpected outcomes] in the competition's history.
The "shock" refers to Germany's early defeat. As defending champions, it is surprising that they have been eliminated so early in the tournament. The expectation was for the defending champions to last longer.
"In one of the [noun]..." indicates that there are multiple such [nouns] in the history of the World Cup, and this is a single example. There have been other "shocks" or surprises in past World Cups, but this (to the author or fans, at least) stands out among them as "one of" the most significant.
Is the use of the preposition "in" what's confusing?
This use of "in" (often said by a 3rd person) explains or characterizes some event:
"In defeat, he found renewed courage"
"In a shocking turn of events, the man blurted out his guilt in front of the entire courtroom."