A total of 21 people died and hundreds were arrested in the week-long protests which were the biggest challenge to the Islamic regime since the 2009 mass demonstrations.
"We cannot accept that some countries -- foremost the US, Israel -- to interfere in the internal affairs of Iran and Pakistan," Erdogan told reporters before heading on a trip to France.
"It is turning the people against each other in these countries. It's a shame that we have seen this done in many nations... We saw this in Iraq."
The Turkish president then referred to problems in "Syria, Palestine, Egypt, Libya and Tunisia" and in African countries including Sudan and Chad.
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He claimed a "game was being played" in certain countries, which he noted were all Muslim-majority nations.
"They are taking steps towards making the plentiful underground riches in all these countries their own resources," he said.
"Sorry, these realities should be known by our people and all people," he said.
Erdogan today praised Rouhani's statements that the street protests were the people's "democratic right", saying this had helped normalise the situation.
Turkey's conservative media had previously accused the US and Israel of stoking the Iran protests as part of a purported plot to transform the Middle East.
Erdogan has on occasion criticised Iran's "Persian imperialism" in the Middle East amid bouts of tension in the Turkey-Iran relationship.
But relations between Ankara and Tehran have warmed since the two countries worked closely with Russia in the last few months to bring peace to Syria.