Bilic kept the team's aces firmly up his sleeve and the eight second-string players who started the match took full advantage with a flawless first-half performance.
"Everyone played well and it will be an extremely tough decision which four players to leave out in the final cut," Bilic told Croatian television.
"It will depend on injuries and our assessment where we need cover. Everyone is still in with a fair chance after a very good acid test for our Euro 2012 opener against Ireland in Poznan on June 10," said the 43-year old coach.
With the likes of Luka Modric watching from the VIP box, Croatia poured forward from the kick off and the midfielder's Tottenham Hotspur team mate Vedran Corluka fired Croatia into a 16th-minute lead.
The central defender volleyed home from close range a low cross from the right by Ivo Ilicevic, who may have been included in the provisional squad to make up the numbers but might well have cemented his place after an effervescent performance.
Nikola Kalinic, another player battling to break into the Euro 2012 squad, made it 2-0 four minutes later with a tap-in.
Halftime substitutions saw several of Croatia's stalwarts enter the fray and two of them produced a superb third in the 81st minute when Ognjen Vukojevic capped a flowing move initiated by Niko Kranjcar.
Konstantin Vassiljev scored a consolation for Estonia with a deflected free kick two minutes later.
Croatia play Norway on June 2 in their final warm-up before they face the Irish in what Bilic described as a crunch Euro 2012 opener in a group including holders Spain and Italy.
"The game against Ireland will be crucial and I am very pleased with our first-half performance against Estonia because these two teams play kindred football," he said.
"Of course, the Irish are a much better team than the Estonians, whom they beat in the playoffs to reach the finals, but the next friendly against Norway will raise the bar and we will move up a gear."