Tudose had himself threatened to resign during a dramatic six-hour meeting of the governing PSD party's executive late Thursday, but got the resignations of the two ministers in the end, according to reports from Bucharest.
Sevil Shhaideh and Rovana Plumb, regional development minister and European funds minister respectively, are allies of party chairman Liviu Dragnea, who in 2016 became ineligible to run for premier due to a vote-rigging conviction.
Past government attempts to weaken probes led early this year to large anti-corruption protests that were backed by centrist President Klaus Iohannis, who has powers to approve premiers.
Analysts said the Social Democrats accepted the reshuffle rather than risk a search for a third prime minister in a few months.
PSD party members said a third resignation involved transport minister Razvan Cuc, who has been accused of taking too long to implement infrastructure projects.
Land transfer probe
In September, anti-corruption prosecutors said they were investigating Shhaideh and Plumb over 324 hectares (800 acres) of Danube riverbank land transferred in 2013 to the Teleorman county council and then leased to a private company.
Both have denied wrongdoing in the case closely watched by the EU's executive commission in Brussels.
Dragnea headed the Teleorman council for more than a decade until 2012 and has reportedly had business ties to the region.
Earlier in the week, Tudose said the corruption allegations surrounding Shhaideh and Plumb had created problems with the European Commission.
'Reality and perception'
"We have a reality and a perception," Tudose said. "The reality is the presumption of innocence, but the perception in Brussels is a different position."
The reshuffle, due to be finalized on Friday, follows the toppling of the ruling coalition's previous premier, Sorin Grindeanu, in June.
Transparency International ranks Romania as one of the most corrupt EU member nations. Brussels has its justice system under special monitoring.
ipj/bk (Reuters, dpa, AP)