The answer is threefold:
Japan and Germany did not coordinate closely. Operation Barbarossa was largely a surprise for Japan.
In 1939, Japan had suffered a disastrous defeat to Soviet forces in Mongolia. Khalkhin Gol, or the Nomonhan Incident, resulted in Japan largely deciding against military action against the Soviet Union for the immediate future.
The third item is perhaps the most important. Logistically, attacking the Soviet Union didn't resolve Japan's immediate issues. Japan's principle reason for going to war against the Western Allies in December 1941 was a lack of immediately available oil. The American oil embargo threatened to cripple Japan's military and much of its economy. Unless Japan could come up with some other source of oil ─ as the Dutch East Indies were ─ it would be forced into a humiliating diplomatic retreat. While attacking the Soviet Union promised to secure undeveloped oil fields in Asia, Japan needed developed oil fields available immediately. The oil fields in Siberia were decades away from production, and that with intensive development.