Why the title "Second Season"? So, the Monogatari series has four season, and soon will be five, and if we look at the production order, based on this question, and this Wikipedia page it will be: 


Bakemonogatari (2009–2010)
Nisemonogatari (2012)
Nekomonogatari (Kuro) (2012)
Monogatari Series: Second Season (2013)
Monogatari Series: Second Season + α or Hanamonogatari (2014)


As you can see, "Second Season" is the fourth and fifth season of anime, so why the title "Second Season"?
Second Season refers to the light novel series, not the anime

The word Second in the anime title Monogatari Series: Second Season is not based on the number of times the series has been animated (which is the usual practice), but rather based on the fact that the anime adapts the content from the Second Season of the Monogatari Series, which consists of 6 volumes (listed in order of publication): Nekomonogatari (White), Kabukimonogatari, Hanamonogatari, Otorimonogatari, Onimonogatari, and Koimonogatari.

The anime Monogatari Series: Second Season (summer 2013) has adapted (listed in airing order) Nekomonogatari (White), Kabukimonogatari, Otorimonogatari, Onimonogatari, Koimonogatari. And this summer (2014), Hanamonogatari will be animated under the title Monogatari Series: Second Season Hanamonogatari.

Earliest usage of the term

The term Second Season has been in used since mid 2011 in Monogatari Series article on Wikipedia.

It also has been used on an anime news site in March 2011, regarding the release of Hanamonogatari (emphasis mine).


  第変話「するがデビル」を収録した西尾維新『花物語』の発売日が3月29日に決まった。『花物語』は化物語シリーズ セカンドシーズン『猫物語(白)』『傾物語』に次ぐ第3弾。


How the term comes to use

As for why the 6 volumes are collectively called Second Season, according to Wikipedia article of Monogatari Series in Japanese:


  『猫物語（黒）』で当初の予定であった暦とその周辺の人物の物語は一通り終了したが、『化物語』のアニメ化に触発されて「セカンドシーズン」が発表された。




My own translation1:

1 Feel free to edit in a correct translation.


  Although the series was initially planned to end at Nekomonogatari (White), at which point the series have finished telling the story about Koyomi and all the people around him, Nishio Ishin was inspired by the anime adaptation of Bakemonogatari and announced the "Second Season".


The old version of the article noted the date of the announcement being June 2010.

Then, Bakemonogatari (2 volumes), Kizumonogatari, Nisemonogatari (2 volumes), Nekomonogatari (Black) are collectively called First Season for the sake of convenience after the Second Season was announced.


  セカンドシーズン発表後に便宜上「ファーストシーズン」と呼ばれるようになった。


Unfortunately, the article (old or new) didn't cite any source regarding the announcement of the Second Season of the novel.

Reference


〈物語〉シリーズ - Wikipedia. Version July 21st, 2014.
〈物語〉シリーズ - Wikipedia. Version July 7th, 2011.