Wong tweeted that he and three others were found not guilty. It's the first verdict in a number of court trials Wong is facing.
The 19-year-old activist captured world headlines when he led pro-democracy street protests in late 2014 against Beijing's decision to restrict elections in Hong Kong, a semiautonomous Chinese region.
The obstruction charges, which carried a maximum two-year sentence, stemmed from a separate protest months earlier in which Wong and the others set fire to an oversized cardboard prop representing a "white paper" policy document issued by China's communist leaders.
Prosecutors said police officers moved in to try to douse the flames with bottles of water but were blocked by Wong and another student protest leader, Nathan Law, according to local media reports. However, the defense team argued that they were pushed from behind by the crowd and couldn't hear police, the reports said.
Wong is also accused in a separate trial of inciting student demonstrators to storm a courtyard at Hong Kong government headquarters in September 2014, leading to a standoff between thousands of supporters and police, who responded with tear gas. The verdict in that case is expected at the end of the month.
He also faces trial on contempt charges for allegedly blocking police trying to clear a protest zone in Hong Kong's Mong Kok district in November 2014.