In Tel Aviv, demonstrators marched to "stop the boycott and the siege of the Palestinian people", referring to international sanctions on the Hamas-led government and Israeli military actions in the territories.
Organisers say about 2,000 people took part on Saturday's demonstration; police said the figure was 500.
Demonstrators met in Rabin Square, Tel Aviv, and marched through central streets to a rally at the Israeli museum, opposite the Israel army's intelligence base in the city.
Protesters carried placards reading, "Negotiations with Palestinian people now!" and chanted: "Occupation, No; Peace, Yes."
Speakers at the rally focused on Israeli policies in the territories and the need for Israel and the western countries to recognise the democratically elected Hamas government.
Shulamit Aloni, an Israeli former minister, said: "There is someone to talk with and we have to talk with them."
Tamer Nafer, of the Palestinian rap band DAM, who performed at the rally, was critical of the event banners referring to 39 years of occupation.
"It should be 58 years, just a small change," said the rapper from Lod, near Tel Aviv, referring to the establishment of Israel in 1948.
Protesters were disappointed by the low turnout, but commented that more young and Arab protesters were visible at yesterday's demonstration.
People took to the streets in
Ram Allah and Tel Aviv
"There are not enough people here, but I am very happy that for one hour there is Arabic heard on the streets of Tel Aviv," said Efrat Noy, from Jerusalem.
Throughout the event, protesters were relayed messages of support from the concurrent demonstration in Ram Allah, which organisers say drew 1,500 people.
In the West Bank city, speakers called for unity between Palestinian factions, and for the blockade on the Palestinian people to be removed.
The Tel Aviv rally, organised by a coalition of 13 Israel left-wing groups, comes days ahead of occupation day, which on June 6 this year marks 39 years since Israel took control of the West Bank and Gaza.
But the demonstration was not supported by Peace Now, Israel's largest left-wing movement.
"The rally's message is not our message," Peace Now's spokesman told an Israel newspaper, adding that the rally should also call on Hamas to recognise Israel.
The rally was also an opportunity to raise funds for an aid delivery to Nablus, that will take place next Saturday.
Campaigners say that tens of thousands of dollars have already been raised to take food and medical supplies to the West Bank city.