Gus Frerotte threw two touchdown passes to Chris Chambers in the third quarter and the Dolphins won their third straight to remain alive for the AFC East title.
"We just came out flat," star tight end Antonio Gates said. "We didn't come out playing Charger football. That led them to believe that they can take this game, which they did. Anytime you let a good team like Miami hang around, one or two plays can change a game, and that's exactly what happened."
On paper, this was the most winnable of the last four games for the defending AFC West champion Chargers (8-5).
"Do we have a tough road? Sure," said Schottenheimer, who ceaselessly preaches the one-game-at-a-time cliche. "But this game doesn't define the season."
"Yeah, I think they were looking ahead," said free safety Yeremiah Bell, who forced a critical fumble by Drew Brees late in the game. "Getting a feeling from them, I don't think they really looked at us as competition. They looked like we were just going to come up here and roll over. But we're not going to do that."
Gates caught an 8-yard TD pass from Brees with 15 seconds left, but the Dolphins recovered the onside kick.
Chambers was the hero of Miami's 24-23 win against Buffalo a week earlier, in which the Dolphins rallied for 21 points in the fourth quarter. He caught 15 passes for 238 yards, both team records, and scored the winning touchdown with a leaping 4-yard reception on fourth down with six seconds left.
He had eight catches for 121 yards against San Diego. Frerotte was 14 of 22 for 229 yards.
The Dolphins held LaDainian Tomlinson to 75 yards on 21 carries and no TDs. Brees was 35 of 52, both career highs, for 279 yards and two TDs, with one interception. Gates had a career-high 13 catches for 123 yards.
Frerotte's 35-yard pass to Chambers put the Dolphins ahead 20-7 with 3:26 left in the quarter, capping a six-play, 87-yard drive. Chambers burned Drayton Florence and was wide open in the end zone.
"Every team has a weakness, and that team, the secondary is a weakness, and that's what we tried to exploit," Frerotte said.
Chambers had more than 100 yards receiving for the third straight game.
"I am in a great rhythm right now," Chambers said. "I am seeing the field a lot better the last half of the season and the chemistry of the whole offense is starting to get better."
San Diego closed to 20-14 with 10:34 left when Brees scored on a 4-yard quarterback draw.
Frerotte came right back, hitting Marty Booker on a 56-yard pass to the San Diego 9, but rookie Ronnie Brown fumbled at the 1 three plays later when he flipped over the pile, with San Diego's Clinton Hart recovering.
Mare also kicked a 29-yard field goal late in the second quarter and the Dolphins trailed just 7-3 at halftime, and added a 20-yarder with 1:11 left in the game.
San Diego took a 7-0 lead on Brees' 8-yard pass to Keenan McCardell late in the first quarter.