Ordering reformers to halt a battle with hardliners over a candidate blacklist on Sunday, Khamenei addressed his comments to President Muhammad Khatami and parliamentary speaker Mahdi Karubi.
The Ayat Allah urged the president to ensure the 20 February polls are "lively and enthusiastic" after Khatami lashed out at the hardliners, saying they would be judged harshly by history.
"Our country today more than any time, needs unity and concord among the esteemed officials," Khamenei said in a letter to the two reform leaders.
"The elections have vital importance for ... the country and our nation and must be held in a healthy, lively and enthusiastic [climate]," he said in the letter published by the government-run news agency IRNA.
The order ends all official avenues of appeal for reformers who accuse hardliners of launching a "coup" by barring thousands of their candidates from the elections for the 290-seat majlis.
On Saturday, Khatami and Karubi wrote to Khamenei complaining that the Guardians Council - an unelected body with sweeping powers which blacklisted the candidates for allegedly disrespecting Islam or the constitution - had reinstated too few in response to his calls for a review.
They warned the narrowed field would make the elections "less competitive" - some constituencies could have only conservative-backed candidates - and make weary voters even more disillusioned.
Khatami's brother said his party
will boycott February's elections
Among those still barred are 75 sitting MPs, including such high-profile politicians as Muhammad Reza Khatami, the president's brother and leader of Iran's biggest pro-reform party - the Islamic Iran Participation Front.
Some 120 MPs, along with some provincial governors and ministers, have also resigned over the blacklist, sparking threats of prosecution from hardliners.
A visibly frustrated Khatami did not hide his bitterness.
"Those in power whose power doesn't come from the people, but who work against them, who use religion, science and even culture to reinforce their power and humiliate others, who deform history ... will be judged mercilessly by history," he told a conference in Tehran.
Khatami's party, the Association of Combatant Clerics, as well as the Servants of Construction - supporters of influential former president Akbar Hashemi Rafsanjani - are expected to decide later on Sunday whether to take part in the elections.
The Islamic Iran Participation Front and Muhajidin of the Islamic Revolution have already said they will stay away.
The interior ministry confirmed it would start preparations for the polls, but said it was still concerned there would be unfair competition in "numerous constituencies."