First-half goals from Andriy Yarmolenko, Oleg Gusev (penalty) and Andriy Voronin had the game wrapped up before the interval, with substitute Artem Milevskiy adding gloss to the scoreline within five minutes of the restart.
The triumph was a fifth in six games for Oleg Blokhin's side, who have had only friendlies to fine-tune plans for their Euro 2012 opener against Sweden on June 11 due to not having had to qualify.
The Ukrainians asserted their authority from the outset at Kufstein Arena and almost went ahead in the first minute, when Yevgen Konoplianka's left-footed blast was parried by Estonia goalkeeper Mihkel Aksalu.
They did not have to wait long to go ahead, though, as Yarmolenko latched onto Serhiy Nazarenko's pass eight minutes later and lashed an unstoppable shot into the top-right corner.
Estonia, who only missed out on a place in Poland and Ukraine in a play-off against Republic of Ireland, offered little as an attacking force and Aksalu continued to be much the busier of the two keepers as the match wore on.
He did well to keep out a Nazarenko drive in the 30th minute but was powerless to keep out Gusev's spot-kick four minutes later after Yarmolenko had been fouled by Ragnar Klavan.
Marko Devic was also denied soon after, Aksalu tipping his effort around the post, before Voronin headed home Devic's cross four minutes before half-time.
Both sides made four substitutions at the break and two of Ukraine's replacements wasted little time making their impact in the second half, Milevskiy slotting his close-range shot into the bottom-left corner from Andriy Shevchenko's pass in the 50th minute.
Ukraine goalkeeper Andrei Pyatov was finally called into action three minutes later to tip a powerful attempt from Tarmo Kink over the bar, but that was as good as it got for Estonia.