Dynamo Kiev midfielders Andrei Yarmolenko and Oleg Gusev scored one each, while forwards Andriy Voronin and Artem Milevsky were also on target.
Ukraine started without veteran star striker Andriy Shevchenko, but nevertheless dominated from the outset and in the ninth minute Yarmolenko fired home the first from 13 metres out following a Sergei Nazarenko pass.
Gusev made it 2-0 after 34 minutes when he converted a penalty after Estonia skipper Ragnar Klavan fouled Yarmolenko in the area.
Voronin grabbed the third four minutes before the break sending the ball into the net with a close-range header from Marko Devic's right-handed cross.
After the interval Ukraine manager Oleg Blokhin substituted Yarmolenko for Shevchenko, who outplayed two Estonian defenders and fed another halftime substitute Milevsky, who rounded off the scoring in the 50th minute.