"As a result of the persistence of regime officials, I allowed it, yet they (the negotiators) crossed the red lines, and the president of the republic confessed to me saying: "if it weren't for the restrictions you imposed, we would have made more concessions," he added.
Several European companies have suspended plans to invest in Iran in light of the US sanctions, including oil major Total as well as carmakers PSA, Renault and Daimler.
Khamenei's comments also sought to downplay the impact of United States sanctions, seemingly an attempt to address protests over Iran's economic woes, Khamenei blamed government mismanagement of the economy for the struggles, not United States sanctions.
Iran's judiciary says the authorities have arrested 67 people in a drive against financial crime as the country faces renewed US sanctions and public outcry against widespread corruption.
He said better economic management would have allowed Iran to resist and overcome the United States blockade.
"With better management and more efficient planning we can resist the sanctions and overcome them", Khamenei said, in an apparent effort to deflect public anger over the deteriorating economy toward Rouhani's government.
Khamenei referred specifically to the collapse in the currency, which has seen half its value wiped since early April.
The rial currency has lost about half of its value since April under the threat of revived US sanctions, with heavy demand for dollars among ordinary Iranians trying to protect their savings.
A fortnight ago, Guards commander Mohammad Ali Jafari told Rouhani to take "revolutionary actions to control prices and prevent the enormous increase in the price of foreign currency and gold", in an open letter published by the conservative Tasnim news agency. The sanctions target Iran's trade in gold and other precious metals, its purchases of USA dollars and its auto industry.
European countries, which still back the 2015 deal, fear Trump's moves will undermine Rouhani and strengthen the hand of his hardline rivals in the clerical establishment.
"The corrupt people [officials] should be punished firmly", Khamenei said on Monday.
Protests in cities and towns across Iran have often begun with slogans against the high cost of living, high prices and a lack of jobs, but have then quickly turned into anti-government rallies.