Zelin, 59, had been in the top military post for five years, during which the air force begun to receive new aircraft and equipment in significant numbers.
No reason was given for the dismissal but senior military commanders in Russia usually retire at age 60.
Igor Korotchenko, chairman of the defence ministry's Public Council said the reshuffle was a normal practice for military officials.
"Medevedev's move will give the road to new, younger military specialists," he said, adding that the experienced Zelin would likely move on to a top post in a defence industrial holding.
"To the observer, Zelin appeared to preside over a period where air force procurement and plans became more planted in reality than merely in aspirations," said Douglas Barrie, an air warfare analyst at the London-based International Institute of Strategic Studies.