Despite initially planning to go ahead with fixtures across the weekend, the Premier League and EFL announced that matches had been postponed until at least 3 April.
The decision brought England's competitions in line with the rest of the major European leagues, with Ligue 1 having been suspended indefinitely while LaLiga and Serie A are off until April at the earliest – the Bundesliga has also been postponed.
Derby County forward Rooney - who is Manchester United and England's record scorer - believes the right decision was taken, though he was left frustrated by how long the authorities took to make the call.
"After the emergency meeting, at last the right decision was made," Rooney wrote in a column in The Times. "Until then it almost felt like footballers in England were being treated like guinea pigs.
"The rest of sport - tennis, Formula One, rugby, golf, football in other countries - was closing down and we were being told to carry on.
"At Derby County, we sat at training on Thursday waiting for [prime minister] Boris Johnson to speak. People were anxious.
"Thankfully football made the right call in the end. We had to put the season on hold. Some people won't be happy but I just think, in this case, football has to come second. It's a sport. It's just a sport."
It remains unclear how the season will continue when the pandemic is over.
On Wednesday (AEDT), the 55 member nations of UEFA will convene to discuss plans for the Champions League, Europa League and Euro 2020, while the Premier League has called another emergency meeting on Friday (AEDT).
Rooney, though, says players will be happy to go with whatever decision is made, as long as it is safe to play again.
"If people's lives are at risk, that has to come first, regardless of whether you're going to win the league title, whether you're trying to get into Europe or whether you're going to get relegated or promoted," he added.
"We're happy to play until September if the season extends to then, if that's how it has to be. That's our job. As long as we know we're safe to play and it's a safe environment for spectators, we'll play."
On Friday (AEST), Arsenal confirmed manager Mikel Arteta has tested positive for COVID-19, as has Chelsea youngster Callum Hudson-Odoi.