One fatality was identified as a 28-year-old Ukrainian national, The Times of Israel reported.
He was a construction worker. The second person needs to be identified.
The third fatality was among those known to be trapped in the wreckage of the collapsed four-story underground parking garage.
Five people had been pulled alive from the wreckage of the collapsed building site by Monday evening, in what the army called a "vigorous" search and rescue effort. At least 24 were injured in the Monday morning cave-in.
Emergency response personnel continued digging through the night at the collapsed site in the Ramat Hahayal neighborhood in hopes of rescuing the four construction workers still missing, but there had been contact with any of them since late afternoon.
The Israel Defense Forces said 500 soldiers and officers were involved in the efforts alongside a number of civilian organizations.
The midday accident occurred at an underground parking garage that was under construction.
The reason for the collapse was not immediately clear, according to Xinhua.
Police launched a criminal investigation into the collapse, suspecting negligence.
The car park was constructed by Africa-Israel, a construction company based in Israel that won a tender to build to the site from the Tel Aviv municipality.