The New York City FC midfielder and the Toronto FC forward were both left off Italy's 30-man preliminary roster for the tournament, which kicks off next month in France.
“We evaluated him [Pirlo] and Giovinco, it’s normal that if you choose to go and play there [MLS] then you can pay the consequences in footballing terms," Conte said at a press conference on Tuesday.
“We evaluated them technically, we didn’t leave anything to chance. Anyone who thinks otherwise is wrong, we went everywhere to have clear and precise ideas. I picked the 30 who I think will give me the most guarantees.”
Despite Conte's comments, the future Chelsea boss has called both players in to the Italy national team during their time in MLS. Giovinco last appeared for Italy in October's Euro 2016 qualifiers and Pirlo played a pair of Euro 2016 qualifiers for the Azzurri in September.
Giovinco, 29, won the MLS MVP award in 2015 and is off to another fine start in 2016, with eight goals and five assists in the season's first 12 games. Pirlo, 37, will likely see his international career end after amassing 116 caps since making his debut with Italy in 2002.
“We’ve made other choices and you have to accept them and deal with the consequences," Conte said. "Nothing was left to chance."
Italy takes on Belgium, Sweden and Ireland in Group E play, which begins on June 13.