Five of the 14 players Fomenko used in their 2-0 Group C win in Borisov on Thursday were involved in a domestic clash between Ukrainian powerhouses Dynamo Kiev and Shakhtar Donetsk just five days later.
Four players - Kiev's Andriy Yarmolenko and Donetsk trio Oleksandr Kucher, Vyacheslav Shevchuk and Taras Stepanenko - started in both matches, as Fomenko's men scored twice late to earn their first points of qualifying.
Ukraine took the lead in the 82nd minute when Belarus defender Aleksandr Martynovich got the final touch into his own net, before substitute Serhiy Sydorchuk scored a sealer in injury time.
Sydorchuk was one of the quintet who started in the Kiev-Donetsk game at the weekend, and Fomenko hailed the output of his fatigued crew.
"Our players were mentally and physically tired before the game as the match was preceded by the FC Dynamo Kyiv game against FC Shakhtar Donetsk," Fomenko said, as reported by UEFA.com.
"We gathered the squad together three days ago so had very limited time to get ready.
"The players showed full commitment today on the pitch and earned their victory.
"I wouldn't say Belarus surprised us. Today, with modern technology, it is hard for opponents to surprise each other."
The loss left Belarus bottom of the group, but coach Georgi Kondratiev said his side were unlucky not to at least get a draw after producing several chances.
"I can't criticise the boys for their performance. They showed great commitment and determination to get a result," Kondratiev said.
"Ukraine could not score themselves - we helped them. Maybe in the first half we struggled a bit more but then we gained momentum.
"We had opportunities to score, [Egor] Filipenko was close and [Mikhail] Gordeychuk had several chances. Probably we lacked efficiency in our finishing.
"I think a draw would have been a fair result today."
