San Diego conceded 14 penalties for 134 yards Ė more than twice the total New Orleans gave up.
"It's uncharacteristic of our team to have that number of penalties," said Tomlinson.
"It was frustrating and tough to make a big play then look back and see it's a penalty."
Double Olympic gold medallist Rebecca Adlington became an honorary Saint for the day at the coin toss, with weather damp but a massive improvement on that for the NFL's first London fixture last season.
After the teams traded early field goals, Brees was key as the Saints scored 20 points in the space of just over eight minutes in the second quarter.
Olympic gold medallist Rebecca Adlington was one of the star faces
The Texan passer first found Devery Henderson uncovered in the left corner of the endzone with a 12-yard pass.
In a rare occurrence for the NFL, Taylor Mehlhaff failed to add the extra point as his kick bounced off the left upright.
But Usama Young scooped up Darren Sproles's fumble on the ensuing kick-off and Deuce McAllister bashed his way in from a yard out to put the Saints 16-3 up.
Tomlinson, who has been struggling with a toe injury all year, kept his side in the contest, turning a short-yardage play into an exquisite 40 yard run to set up his own score on a pass from Rivers.
Brees was perfect with three pass attempts on the following drive, though, the third finding an overjoyed Lance Moore - again in the left corner - from 30 yards out.
After several miscues, San Diego's passing game finally clicked under Rivers as he found tight end Antonio Gates with 68 seconds left in the half.
Reaction: Chargers v Saints
New Orleans, who gave up a home fixture to allow an NFL regular season game to be played in London for the second year running, appeared to seal the game from there.
Brees found tight-end Mark Campbell from a yard out then full-back John Karney rumbled in for his second score in as many games - and just the fifth of his five-year career.
In between, a touchdown pass from Rivers to Brandon Manumaleuna that would have taken San Diego to within six points at 30-24 in the third quarter, was annulled by a holding call.
But Rivers kept his cool as the New Orleans defence tired for an impressive finale.
New Orleans coach Sean Payton said the quality of the field was poor and blamed it for the struggles endured by his defenders.
He said: "The footing was bad, the field was slick and choppy and generally it comes in favour of offences.
"After our run-through on Saturday we knew it would be a sloppy field regardless of whether it rained."
San Diego coach Norv Turner said: "It was obviously looser than other fields we play on but I donít think it affected the quality of play."
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