On Friday, an Iranian general warned the country could seize a British ship in retaliation.
The tanker remained stationary for a day until it was caught up to by the HMS Montrose and thereafter started moving towards the strait.
Rouhani, however, after meeting with Bonne said "Iran has fully left the path open for diplomacy and negotiation".
"The UK's action was in retaliation of the Iranian Armed Forces' fearless move to down the enemy's intruding drone".
A diplomatic adviser to French President Emmanuel Macron held talks in Tehran Wednesday aimed at saving the 2015 deal.
Baqeri also said that Britain's seizure of the tanker was "act of revenge" in response to Iran's downing of a US drone over the Persian Gulf last month.
Emmanuel Bonne met Rear-Admiral Ali Shamkhani, secretary of Iran's Supreme National Security Council, and was set to meet with Foreign Minister Mohammad Javad Zarif later on Wednesday. In the deal with world powers negotiated by the Obama administration, Iran had agreed to curb its nuclear activities in return for sanctions relief.
The European parties to the deal along with the EU's diplomatic chief on Tuesday called on Tehran to reverse breaches of the agreement.
Iran's Foreign Ministry has summoned the British envoy to Tehran three times since Thursday in protest at the United Kingdom navy's move.
Meanwhile America has begun making plans to enlist allies over the next two weeks into a military coalition to safeguard strategic waters off Iran.
"Escorting in the normal course of events would be done by countries who have the same flag so a ship that is flagged by a particular country would be escorted by that country and I think what the United States can provide is domain awareness, intelligence, surveillance, reconnaissance and then coordination and patrols for other ships that would be in the area would be largely coalition ships", Dunford said. Allies would patrol waters near those US command ships and escort commercial vessels with their nation's flags.