VH-EAN was en route from Sydney to Perth, cruising at flight level (FL)350. N99SC was en route from Essendon to Sydney cruising at FL410 and requiring descent. Both aircraft were under the control of the Melbourne Air Traffic Control Centre, Sector 7. It was apparent that the two aircraft would be in lateral conflict near Yass. The controller cleared N99SC to descend to FL360. Above FL290, for aircraft that are not laterally separated, the minimum vertical separation is 2000 feet. In this instance the controller had only provided 1000 feet. The two aircraft passed with about three and one half miles lateral separation and 1000 feet vertical separation. For aircraft not vertically separated, the minimum lateral separation in this instance was five miles. The controller realised his error but too late to rectify the situation. Investigation revealed that prior to the incident the controller had been busy with aircraft inbound to Sydney, entering the holding pattern at Bindook. All levels assigned to other aircraft had been in the range of FL210 to FL260 where only 1000 feet vertical separation is required. He believed it was this that had led him to inadvertently apply the same standard to VH-EAN and N99SC