Magalona, a host of the noontime variety show Eat Bulaga, and Alfredo de los Santos were previously arrested for possession and use of marijuana.
But Judge Henri Jean-Paul Inting, of the QC RTC Branch 95, cleared Magalona of the drug charges as the prosecution failed to prove the rappers guilt.
In a 16-page decision, Inting said the credibility of the testimonies lodged by arresting officers PO1 Miguel Cordero and PO3 James Bustinera against Magalona were ruined with the negative results of the drug test made on the actor.
Court records showed that Magalona and De los Santos were supposedly caught in the act of smoking pot while inside a Honda CRV last May 29, 2001 in Quezon City.
The police officers insisted that they were able to seize a stick of marijuana from Magalona and his friend.
"This allegations of witness PO1 Miguel Cordero was completely shattered by the evidence. The result of the Drug Dependency Test conducted on the urine sample of the accused Francis Magalona extracted on the same day when the incident happened belied the allegation.
"The said test showed the urine sample of accused Magalona was negative for THC-Metabolites, a component of marijuana," Inting said, even noting the testimony of an expert at the PNP-Crime Laboratory that THC-Metabolites stays in the human body for three to 10 days.
Inting also questioned the manner by which the evidence presented against Magalona was purportedly confiscated.
The arresting officers claimed the respondents were committing a crime in their presence, which authorized them to search the vehicle.
However, this claim was disputed by the defense, asserting that Cordero approached Magalonas car and went to the front passenger side, opened the door and searched the glove compartment despite protests from Magalona.
The policemen then ordered De los Santos to alight from their vehicle. Later Bustinera flashed "a rolled stick of paper," affirming the supposed presence of the contraband.
Inting said the claims of the arresting officers lacked merit since they admitted chasing the respondents before even seeing Magalona smoking marijuana.
"The court finds it difficult to comprehend the allegation of PO3 Bustinera that he was able to recover and confiscate marijuana from the accused. It was a long car chase and later on foot with the accused finally ending up inside a town house," the decision read.
"Granting the accused has an illegal item in his person, it is more in keeping with human behavior and human nature for the accused to have just thrown away that illegal item in his possession," it added.