Malár was during the interwar period one of few successful higher officers of Slovak nationality in Czechoslovak Army. After the German occupation of the Bohemia and Moravia and the establishment of First Slovak Republic in March 1939, he became one of highest and most experienced officers in newly created Slovak army. After the declaring war to USSR, so called Fast moving division - Slovak motorized division was deployed on Eastern Front. Malár became commander of the unit at the turn of 1941 and 1942. During this service he earned promotion to general and German Knight's Cross of the Iron Cross.
Later he served in General staff and in 1944 he was appointed as a commander of East Slovak Army - two best Slovak divisions which should defend Slovakia against Soviet offensives. Planners of insurrection against Nazi rule (Slovak illegal National Council), assumed him as a Slavophile and experienced field commander, to be the leader of the East Slovak units which would fight to connect with Soviets to help them pass through Slovak territory without a fight.
However, after inappropriately timed start of the uprising on August 29, 1944, contrary to expectations, he did not join the rebels. On the contrary in a radio speech next day, he opposed and exhorted soldiers to return to barracks as "our time has not come yet." As a military strategist, he wanted uprising to end successfully.
Because of his words about fight with Germans in the future, German security authorities arrested him when he returned to Prešov in Eastern Slovakia. He was deported to Germany, where he died after interrogation in the Sachsenhausen concentration camp.
- Fellgiebel, Walther-Peer (2000). Die Träger des Ritterkreuzes des Eisernen Kreuzes 1939–1945 – Die Inhaber der höchsten Auszeichnung des Zweiten Weltkrieges aller Wehrmachtsteile [The Bearers of the Knight's Cross of the Iron Cross 1939–1945 — The Owners of the Highest Award of the Second World War of all Wehrmacht Branches] (in German). Friedberg, Germany: Podzun-Pallas. ISBN 978-3-7909-0284-6.