Roethlisberger thrust both fists in the air in celebration from the bench, his left leg wrapped in ice and bandages.
"He laid it on the line," receiver Hines Ward said of the second-year quarterback. "He's lying there hurt on the ground, and he said to me, 'At least we're in field goal range."'
"It looked bad from what I saw up on the screen," Cowher said.
Roethlisberger, whose knee was bent back awkwardly on the hit, was driven off the field on a cart after the final gun.
Roethlisberger was replaced by Charlie Batch, who has played only a handful of downs the last three years. Batch handed off three straight times to Jerome Bettis before Reed's kick.
The Bus carried seven times for 21 yards on the winning drive.
"I went to Charlie and said, 'Give it to me, look it all the way in, follow me as I go through, and I'll do the rest,'" said Bettis, who missed the first three games with a calf injury sustained during the exhibition season.
Roethlisberger ran for one touchdown and threw for another, and Bettis rushed for a TD in his season debut for the Steelers (3-1). San Diego (2-3) had its two-game winning streak snapped.
"I feel great, I feel fresh," Bettis said after scoring a touchdown in his season debut.
San Diego had gone ahead on LaDainian Tomlinson 's 2-yard run with 4:42 left. Tomlinson was stuffed on a two-point conversion attempt that would have given the Chargers a 24-21 lead.
Tomlinson extended his NFL record by scoring a rushing touchdown in 17 straight games.
Stung by a loss to New England 15 days earlier and coming off their bye, the Steelers bounced back with a crisp game by Roethlisberger and the defense, which made Tomlinson and the rest of the San Diego offense look average.
Tomlinson was held to 62 yards on 18 carries. Brees threw his first interception in three games, which set up Bettis' TD run.
"That was probably the best defense I've faced as far as the run game in my career," Tomlinson said.
Roethlisberger gave the Steelers a 21-16 lead on a 16-yard pass to Heath Miller with 10:30 to go. He was impressive on the go-ahead drive, completing it in only three passes. Starting on the Pittsburgh 38, the second-year pro had completions of 33 and 13 yards to Ward before hitting Miller for the touchdown.
Roethlisberger was 17 of 26 passing for 225 yards, with no interceptions. Bettis gained 54 yards on 17 carries.
Bettis and Roethlisberger both scored in the second quarter. On third-and-5 from the Chargers 7, Roethlisberger lined up in the shotgun, took the snap and scrambled into the end zone.
His TD came four plays after his apparent 47-yard touchdown pass to Hines Ward was overturned after a challenge by Chargers coach Marty Schottenheimer.
Bettis scored on a 1-yard run. which capped a drive set up when James Harrison intercepted Brees, hurdled Tomlinson and gained 25 yards before being tripped up by Brees. An unnecessary roughness call against Chargers guard Kris Dielman added 15 yards.
San Diego pulled to 14-7 on an 11-yard scoring pass from Brees to Gates with 34 seconds left before halftime. That drive started after a 48-yard kickoff return by rookie Darren Sproles.
The Chargers had gone ahead 16-14 on Nate Kaeding's third field goal of the second half, from 41 yards with 11:41 to play. Kaeding also had field goals of 34 and 32 yards in the third quarter.
Kaeding's 32-yarder, with 3:54 left in the third, came one play after Willie Williams broke up a pass from Brees to Gates in the end zone.