Kenya responded swiftly, with Job Ochieng making a surging run down the flank before cutting inside and unleashing a powerful effort that was well blocked by Tanel Tammik.
Estonia continued to press and nearly found the breakthrough through Markus Poom, who rose to meet a delivery from Patrick Kristal but failed to hit the target.
Their persistence paid off minutes later when Joonas Tammik powered home a header from Alex Matthias Männilaan’s cross to hand the Europeans a deserved lead just past the quarter-hour mark.
Kenya responded with urgency. Ryan Ogam came close moments later, failing to connect cleanly with a teasing delivery from Ochieng.
The forward had another golden opportunity midway through the half, but saw his low drive comfortably gathered by Rauno Sappinen in goal.
Further chances fell Kenya’s way, with William Lenkupae narrowly missing the target with a header, while Ochieng thought he had equalized late in the half, only for his effort to be ruled out for offside.
Ogam then struck the woodwork in the closing minutes, as Estonia went into the break holding a slender advantage.
Harambee Stars returned for the second half with renewed intensity and were duly rewarded ten minutes after the restart.
Zech Obiero delivered a precise lofted pass that found Ogam, who made no mistake in calmly slotting home to restore parity.
Kenya pushed for a winner, with Obiero and substitute Lawrence Okoth both going close, while Austin Odhiambo also tested the Estonian defense with a late effort that drifted narrowly off target.
Estonia, however, remained dangerous on the counter, with Joonas Tammik and substitute Sergei Yakovlev both threatening, but Kenya’s defense, marshaled by Aphonce Omija, held firm.
With neither side able to find a decisive goal in regulation time, the match was settled via penalties.
Erko Jonne Tõugjas, Michael Schjønning-Larsen, Alex Matthias Tamm, Rauno Sappinen and Markus Soomets were on target for Estonia. Ian Otieno saved Ioan Yakovlev’s kick.
Kenya’s hopes were dented when Mohamed Bajaber missed his effort, and although Austin Odhiambo,Lawrence Ouma Chris Erambo and Ben Stanley kept the hosts in contention, the decisive moment came when Richard Odada’s attempted Panenka sailed over the bar, handing Estonia a 5-4 shootout victory.
The win sees Estonia advance to the final of the mini-tournament, while Kenya will now face the loser between Rwanda and Grenada in the third-place playoff.