This punishment sent out a message to all teams of the importance of maintaining a healthy pace throughout a match
Danny Ings produced two fine finishes to further his case for the Premier League Golden Boot as Saints realistically secured their top-flight status for another season by reaching 40 points.
A bad day for the Hornets began before kick-off when three players were excluded from Pearson's squad for breaching coronavirus protocols.
Watford said Andre Gray, Nathaniel Chalobah and Domingos Quina were not included to protect "the health and safety of all players, staff and officials" after Gray hosted a birthday party on Friday with more than the permitted six people present.
On the field, Pearson's men have also had a poor start to the Premier League resumption with just one point from their first three games leaving them still just a point above the drop zone.
"We were second best for too long," said Pearson. "You can't concede goals like gifts to your opponents, it makes the job even harder."
Watford are the only side this season to beat champions Liverpool in the Premier League and also beat Manchester United early in Pearson's reign after taking charge in December.
With bottom-of-the-table Norwich, Newcastle and fellow strugglers West Ham to come in three of his side's next four games, Pearson remains confident Watford will be safe if they find their best form.
"We are not achieving the types of performances we know we are capable of," he added. "We have games left where it is in our own hands, where we can assure our own future in the Premier League."
Ings could have been representing England this month at Euro 2020 had the coronavirus pandemic not delayed that tournament for a year, but he has picked up where he left off before the three-month stoppage.
The former Liverpool forward brilliantly made space for himself on the edge of the box before curling into the far corner on 16 minutes to give Saints a deserved first-half lead.
Watford gave themselves a mountain to climb when Ben Foster's poor throw was pounced upon by Ings to drill home his 18th Premier League goal of the season and move within one of Jamie Vardy as the top scorer in the division.
"I just want to score as many goals as I can," said Ings on his chances of beating out the likes of Vardy, Pierre-Emerick Aubameyang, Mohamed Salah and Sadio Mane to the Golden Boot.
Jan Bednarek's own goal briefly gave the hosts hope of a comeback.
However, Southampton restored their two-goal advantage within three minutes as James Ward-Prowse curled a brilliant free-kick into the top corner.
This punishment sent out a message to all teams of the importance of maintaining a healthy pace throughout a match
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