Modric is in the middle of a protracted move to Real Madrid and Stimac, who took over from Slaven Bilic after the team's early Euro 2012 exit, said "time was running out" for the player ahead of the ties against Macedonia on September 7 and Belgium four days later.
"We can't carry the burden of his dilemma for him," Stimac told a news conference after including the Spurs playmaker in his squad.
"As the coach I will not allow the question of whether one particular player is fit to play or not to become the focus of attention ahead of two vital World Cup qualifiers."
Modric has not played for Spurs yet this season and is in a state of isolation at the Premier League club.
Stimac, who came under fire from media and fans after a 4-2 defeat by Switzerland in last week's friendly in Split, has dropped left-back Danijel Pranjic and called up uncapped midfielder Josip Radosevic to his squad.
He also left out Dinamo Zagreb's Brazilian-born forward Sammir after including seven strikers in his squad.
"I would be delighted if Sammir was up to the national team's standards at this point in time but he is not," said the 44-year-old coach.
Group A also includes Serbia, Scotland and Wales.
Goalkeepers: Stipe Pletikosa (Rostov), Danijel Subasic (Monaco), Ivan Kelava (Dinamo Zagreb).
Defenders: Darijo Srna (Shaktar Donetsk), Vedran Corluka (Lokomotive Moscow), Ivan Strinic (Dnipro Dnipropetrovsk), Josip Simunic (Dinamo Zagreb), Domagoj Vida (Dinamo Zagreb), Gordon Schildenfeld (Dinamo Moscow), Dejan Lovren (Olympique Lyon), Manuel Pamic (Sparta Prague).
Midfielders: Luka Modric (Tottenham Hotspur), Niko Kranjcar (Dynamo Kiev), Ognjen Vukojevic (Dynamo Kiev), Ivan Perisic (Borussia Dortmund), Ivan Rakitic (Sevilla), Milan Badelj (Dinamo Zagreb), Ivo Ilicevic (Hamburg SV), Josip Radosevic (Hajduk Split).
Forwards: Mario Mandzukic (Bayern Munich), Ivica Olic (Hamburg SV), Nikica Jelavic (Everton), Eduardo da Silva (Shakhtar Donetsk), Mladen Petric (Fulham), Nikola Kalinic (Dnipro Dnipropetrovsk), Ante Vukusic (Hajduk Split).
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