A motion to override the veto received 244 votes in favour, with 180 against and 16 abstentions—short of the three-fifths majority required.
The vote followed a heated and politically charged debate, with lawmakers trading sharp exchanges ahead of the session.
Before the vote, Prime Minister Donald Tusk urged lawmakers to reject the veto, arguing that the Code of Criminal Procedure needed reform after years of what he described as "damaging justice policies" under the previous right-wing government.
The bill would have barred the use of unlawfully obtained evidence, including material gathered through criminal acts such as illegal wiretapping.
It also sought to limit the use of pre-trial detention, strengthen defence rights at an early stage of proceedings, protect confidential contact between suspects and lawyers, and shift more procedural authority from prosecutors to courts, state news agency PAP reported.
Under the proposal, the prospect of a severe sentence alone would, in many cases, no longer justify pre-trial detention.
Nawrocki vetoed the bill in mid-March. His office said the decision was driven by concerns over public safety and the state's ability to combat serious crime.
Presidential aides also argued that some of the proposed changes could make criminal proceedings more difficult.
The veto has sparked an unusual backlash from hard-core soccer fans, with supporter groups at several stadiums protesting last weekend, arguing that current rules allow suspects to be held for long periods without sufficient evidence.
Zbigniew Bogucki, head of the president’s office, told lawmakers that Nawrocki submitted his own bill on Friday proposing measures to address prolonged pre-trial detention.
Under Polish law, the lower house can override a presidential veto with a three-fifths majority in the presence of at least half of all lawmakers. If all 460 deputies are present, 276 votes are required.