There was a certain amount of cooperation between Germany and Japan at sea. Before Japan entered the war, several German auxiliary cruisers operated in the Pacific and Indian oceans. These were armed merchant ships, which struck at British and Commonwealth shipping in those regions. They saw a certain amount of success, with the Kormoran sinking the Australian light cruiser HMAS Sydney on the 19th November 1941, although she would sink due to damage taken in that engagement. Easily their most significant success was the capture of the SS Automedon by Atlantis. The Automedon was a British merchantman, carrying, amongst other items, mail to the British Far East Command at Singapore from the War Ministry's Planning Division. This contained significant information about British plans for the defense of Singapore, Malaysia and the Dutch East Indies. This was passed by the commander of Atlantis to the Japanese authorities, and influenced the Singapore Campaign once Japan entered the war.

After December 7th 1941, the main point of contact between Japanese and German forces came in the form of submarines. From the summer of 1942, Japanese, German and Italian submarines travelled between Europe and Japan carrying various strategic materials, ranging from blueprints to uranium oxide. In May 1943, the Germans began to establish a submarine base at Penang, on the Indian Ocean coast of Malaysia. Submarines operating from here fought almost entirely in the Indian Ocean, and have become known in the literature as the Monsoon Group (Gruppe Monsun), after a wolfpack organised there in 1943. The website uboat.net has a decent article about them here.