Describing the action of Abu Ali as "unacceptable", the MEA said India's concerns "were conveyed both in New Delhi to the Palestinian ambassador and in Ramallah to the minister of foreign affairs and expatriates".
"Palestine is keen to maintain good relations with friendly India and supports it for the efforts in its fight against terrorism", the Palestine Foreign Office spokesperson said.
Palestinian envoy Walid Abu Ali shared the stage with Hafiz Saeed, the head of the hard-line Jamaat-ud-Dawa movement, at Friday's rally, which was held to protest US recognition of Jerusalem as Israel's capital.
In New Delhi, Palestine's envoy Adnan Abu Alhaijaa said that there were some politicians and parliamentarians attending the event.
A statement issued by India's external affairs ministry said the Palestinian side "conveyed deep regrets over the incident and assured the government of India that they are taking serious cognisance of their ambassador's presence" at the rally.
India was told Palestine would not "engage with those who commit acts of terror against India".
India issued a strongly worded demarche after photos of Walid Abu Ali sharing the stage with Saeed and addressing the rally organised by the Difa-e-Pakistan Council (DPC) were circulated on social media on Friday.
What followed was a calculated measure from Palestine, who said, "it was an unintended mistake, but not justified".
"The public meeting held yesterday was yet another demonstration of the Pakistani strong sentiments in support of the Palestinian cause", said a foreign ministry statement.
The statement further said: "We take note of the assurances given by the Palestine side". The countries disregarded Trump's threat to cut aid to the countries that voted for the resolution.
Alhaijaa has been coordinating with the Indian government to schedule a possible visit by Prime Minister Narendra Modi to Palestine.
The Palestinian foreign ministry in its statement said Palestine "highly appreciates" the move by India to vote in favour of a resolution asking the U.S. to withdraw its decision to recognise Jerusalem as the Israeli capital at the United Nations General Assembly.
Palestinian envoy who shared dais with Hafiz Saeed recalled.
Late on Saturday, Pakistan defended the decision to allow Saeed's rally in Rawalpindi. "In fact, when Saeed spoke, he asked people around him who he was.He did not know the terrorist personally". It has campaigned for long for snapping ties with India and the US. India had made a decision to vote along with the principled position taken by New Delhi for the last seven decades, despite the BJP-led NDA government taking steps to strengthen bilateral relations with Israel. His appearance and support for Pakistan - and Pakistani terrorists - was seen as a major slap in the face to India.