After graduating from a lyceum of Stanisław Konarski, he joined the high school of Hipolit Wawelberg, the only institution of higher education in Warsaw to allow Polish language (though not openly).

During that time he joined the Związek Walki Czynnej, a secret Polish anti-tsarist organization preparing the cadres for a future anti-Russian uprising aimed at liberation of Poland.

After the outbreak of the Invasion of Poland in 1939, during the opening stages of World War II, Kowalski proved to be one of the most successful commanding officers in the Polish Army at that time.

Delaying the German forces in a number of skirmishes and battles along the Narew and near Różan, Kowalski's units managed to retain most of their combat readiness.

After repelling a German assault on Brańszczyk, his forces started to slowly move southwards while performing delaying actions and keeping the combat readiness almost intact.

Despite heavy losses on the Polish side, Wincenty Kowalski managed to yet again rally a large part of his forces and continued his move towards Włodawa, Lublin and Lwów.

Near Chełm, on September 18 and 19th Kowalski's division (then reduced to merely a regiment after two weeks of constant fights against numerically and technically superior enemy) was reorganized and reinforced with an improvised detachment under Stanisław Tatar.

Outnumbered, lacking artillery, supplies, food and reduced to not more than a regiment, the division's assault on Tarnawatka was stopped on 23 September and wounded General Kowalski was taken prisoner of war by the Germans.

After half a year in a prison hospital, in early 1940 Kowalski was transported to Oflag VII-A Murnau POW camp, where he spent the entire war.