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I suspect that today, this achievement has been granted for the first time to Brazil, with the arresting of Michel Temer, and considering that Lula da Silva is still under arrest.

It is normally big news if a former president is incarcerated, so I'd be surprised to know this occurred twice somewhere else.

Peru has an interesting case of former presidents being incarcerated or in the eye of justice.

• 
  Alberto Fujimori in right now in prison, for human right violations, 25 years of conviction.


• 
  Ollanta Humala is in preventive reclusion, investigated for corruption.


• 
  Alejandro Toledo, currently fugitive of justice for corruption as well. Case Oderbrecht (link in Spanish), that started in Brasil.


• 
  Alan García, twice president, twice investigated for corruption. Lately due to case Oderbrecht as well.

Summary, if you have been a Peruvian president, you are probably under investigation by the justice.

Quite a few candidates if:

https://en.wikipedia.org/wiki/List_of_heads_of_regimes_who_were_later_imprisoned

... [sort by country] is anything to go by...

• Andalusia (technically an autonomous community in Spain) appears to have two former presidents sitting in jail since 2016.




• Argentina has a whopping 8 presidents that sat in jail, including 2 from 2007 onward.




• Bangladesh had 5 presidents who went to jail, of which two were behind bars in 1975.




• Bosnia and Herzegovina had 2 presidents sitting in jail from 2006 to 2012.




• Bulgaria had as many as 3 former prime ministers behind bars at the same time in 1944.




• Comoros has 3 presidents and prime ministers behind bars if the article is anything to go by.




• Costa Rica had 2 presidents behind bars from 2004 to 2012.

I'll stop at C, since the list is long, with a few honorable mentions:

• Egypt appears to have had 5 former presidents in jail in 2013.




• Guatemala 3 early in 2018




• Hungary 4 in 1945




• Iraq 4 in 2004




• Japan 5 in 1945




• Libya 4 in 2011




• Pakistan 4 + 2 arrest warrants as I write this

The point is Brazil is not an exception, with one caveat: read the list with a fistful of salt, because it lists former French President Sarkozy as sitting behind bars since 2018, whereas he was only put in police custody for a day that year as he was charged with bribery and illegal campaign contributions. (He might sit in jail some day in the future, but the point here is that you may want to double check the data.) Also, Gaston Flosse of French Polynesia is listed twice.