The league said on Sunday it would start a disciplinary process to investigate if the match complied with health rules.
Benfica took advantage of their numerical superiority to rack up seven goals by halftime before Belenenses returned with only seven players for the second period.
The match was called off two minutes after the break when Joao Monteiro, a goalkeeper playing in midfield, sat down on the ground unable to continue, forcing the referee to abandon the game, which requires a minimum of seven players.
Following one positive COVID-19 test in the squad earlier in the week, a total of 17 cases were reported among Belenenses players and staff, club president Rui Pedro Soares told a news conference on Saturday before the match.
Belenenses players shared a message on social media before the game that said: "Football only has heart if it is competitive. Football only has heart if it is really sporting. Football only has heart when it is an example of public health. Today, football lost its heart."
Soares told reporters he had unsuccessfully asked the authorities for the game to be postponed.
"In the middle of the afternoon we communicated to the Liga that we didn't want to play the game," he said. "We had eight players who could attend the game and as such, they told us that if we didn't attend the game it would be unjustified absence.
"Playing here today was a shame for all of us."
Soares added that he was concerned the cases in the squad could be related to the new Omicron variant. It was first discovered by researchers in South Africa, and the World Health Organisation on Friday classed it as a " variant of concern," saying it may spread more quickly than other forms.
Benfica president Rui Costa said his side had no choice but to play the game on Saturday.
"We did not like to enter the pitch under these conditions," he said. "Benfica was forced to do it like Belenenses. I regret what happened today, a dark chapter for Portuguese football and for the country itself."
Sporting, third in the standings behind leaders Benfica, also released a statement.
"What made this situation possible must deserve a deep reflection by all those who defend the sporting truth and must deserve national attention at the highest level," it said.
"It is already receiving international attention and marking yet another dark episode in Portuguese football."
Responding to the accusations, the Portuguese football league told Lusa news agency they did not receive a formal request to postpone the match.
In a statement, the league said it would open an investigation to determine responsibility, particularly "related to the compliance with sanitary protocols". Its board of directors will hold discussions on Monday.
The league also called emergency meetings with the government and health authority DGS to obtain information on the COVID-19 protocol in place.
Without providing further details, DGS said it does not comment on the football matches. A DGS spokesperson told Reuters it was not up to the health authority to postpone it but to assess the COVID-19 situation and implement measures, such as self-isolation, to stop the spread.