Foreign ministry spokesman Bahram Qasemi said the operation was "over for now" and that the planes had "gone", the BBC reports.
Defense Minister Hossein Deghan had earlier criticized Russia for publicizing the raids last week, saying it had exhibited a "show-off" attitude.
There was no immediate response from Moscow, which like Tehran is a key ally of Syria's President Bashar al-Assad.
Last Tuesday, Russia's defense ministry announced that Tupolev-22M3 long-range bombers and Sukhoi-34 strike fighters had used the Shahid Nojeh airbase near the eastern city of Hamedan to carry out air strikes on "terrorists" in Syria.
The raids were the first carried by Russia from a third country since it began an air campaign against Mr. Assad's opponents almost a year ago, and also the first launched from Iranian soil by a foreign military since World War Two.
The secretary of Iran's Supreme National Security Council, Ali Shamkhani, lauded the "strategic" co-operation with Russia. But some MPs complained that it breached the Islamic Republic's constitution, which prohibits allowing foreign militaries to be based on its territory.
Read alsoRussia deploys jets at Iranian Airbase to combat insurgents in SyriaIn an interview with state TV on Monday, Gen Deghan stressed that Russia would only use the Nojeh airbase "for a very short and fixed span, corresponding [to an] operation in Syria".
Gen Deghan was asked why Russia had chosen to reveal its presence there whereas Iran had not.
"The Russians are interested to show they are a superpower to guarantee their share in the political future of Syria and, of course, there has been a kind of show-off and ungentlemanly [attitude] in this field."
Gen Deghan explained that Russia had "decided to bring in more planes and boost its speed and accuracy in operations".
"Therefore, it needed to refuel in an area closer to the operation. That's why they used the Nojeh base. But we have definitely not given them a military base."
Hours later, Mr. Qasemi announced that Russia's deployment had ended.
"It was a specific, authorized mission and it's over for now. They conducted it and they are gone now," he was quoted by the official news agency as saying.
Future use would depend on "the situation in the region", he added.
The U.S., which backs the opposition to Syria's president, had said Russia's use of the Iranian base was "unfortunate but not surprising".
