Gates put the game out of reach with his third TD, when he caught a short pass at the KC 32, bulled through strong safety Sammy Knight and ran into the end zone for a 28-13 lead with 9:10 left.
"It's like LT. They are both Supermanesque," said Brees, who threw for 324 yards. "We see it in practice every day. Game day, it gets better. I'm lucky to have those two."
Gates had 10 catches for 145 yards, both career highs, and the three TD catches tied his career best. Last year, his 13 TD catches set an NFL record for tight ends.
He has six touchdowns in seven games. He missed the opener while finishing his three-game suspension for missing a team-imposed deadline for ending his training camp holdout.
Gates' big day for the Chargers (4-4) came against a team that features six-time Pro Bowler Tony Gonzalez.
"The guy on the other side is not too shabby," Brees said.
But Brees thinks Gates is the best tight end. "They are 1-2," the QB said. "He showed, or confirmed, that he is the guy."
Asked if he's the NFL's best tight end, Gates deferred to Gonzalez.
"Tony has definitely set a high standard at tight end," Gates said. "He's done it year in and year out. This is just my third year and I'm upcoming. He's been to six Pro Bowls. I have to get to six Pro Bowls to say that."
Gonzalez had seven catches for 97 yards and one score for KC (4-3).
"Any time we play against each other, he makes me elevate my game," Gates said. "That is just the competitive nature about me."
Gonzalez was impressed with Gates.
"I am happy for Antonio. He came out and played great today, one of the best games I have ever seen by a tight end," Gonzalez said.
Gates, a former college basketball star, continues to thrive no matter how teams try to cover him.
"They just get him in a one-on-one situation and he wins that battle," Chiefs coach Dick Vermeil said.
"He is very powerful," Brees said. "You can't really tackle him with one guy. You see him break tackles all the time, like he did on the last touchdown. Obviously his ability to catch the football is special."
Brees completed 25 of 43 passes, with TD throws of 19, 20 and 35 yards to Gates. He also was intercepted once.
Kansas City's Priest Holmes sustained a mild concussion when hit by rookie linebacker Shawne Merriman midway through the third quarter and didn't return. Vermeil said Holmes will be OK.
Tomlinson gained 69 yards on 17 carries a week after being held to a career-low 7 yards in a loss at Philadelphia. He was held without a touchdown for the second straight game.
Green, whose father, Jim, died late last week, was 31-of-43 for 347 yards.
The Chargers stopped the Chiefs at the San Diego 9 late in the game. Green did throw a 7-yard scoring pass to Eddie Kennison with 2:12 left, but the Chargers recovered the onside kick and the Chiefs were out of timeouts.
Gates caught a 19-yard TD pass down the right sideline in the first quarter for a 7-0 lead, then burned linebacker Kawika Mitchell to make a 20-yard scoring catch with 27 seconds left before halftime for a 21-3 lead.
Tomlinson's TD throw to Eric Parker was sandwiched in between. Tomlinson had given the Chargers a first down at the KC 17 with a 13-yard run on the final play of the first quarter. On the next play, he swung out to the right, took a quick toss from Brees and threw to Parker, who was the only player in the end zone.
The Chiefs, particularly cornerback Patrick Surtain, bit so hard when Brees tossed to Tomlinson that Parker didn't have a defender within 10 yards of him.
Tomlinson has thrown four career touchdown passes.
Kansas City's Lawrence Tynes kicked a 34-yard field goal in the second quarter and a 20-yarder in the fourth quarter. Gonzalez caught a 16-yard pass midway through the third quarter to pull the Chiefs to 21-10.
- Tomlinson hasn't gone two straight games without a touchdown since the first two games of the 2003 season.
- Merriman had two sacks and forced a fumble by Green, and rookie DE Luis Castillo had 1 1/2 sacks.
- Players who left with injuries were Chiefs CB Eric Warfield (right hip pointer) and S Jerome Woods (strained right hamstring), and San Diego LT Roman Oben (sprained foot) and S Terrence Kiel (sprained ankle).