KANSAS CITY, Mo. >> Chiefs quarterback Alex Smith struggled against his former team, and backup San Francisco quarterback B.J. Daniels threw a late touchdown pass to give the 49ers a 15-13 victory over Kansas City in a preseason game Friday night.

Phil Dawson hit all three of his field-goal attempts for the 49ers, two of them 55-yarders, while the Chiefs’ Quintin Demps returned a kickoff 104 yards for a touchdown.

Smith was just 7 of 16 for 62 yards while playing the full first half, but he did help Kansas City to two field goals. The 49ers didn’t go easy on him, either: Defensive tackle Tony Jerod-Eddie was flagged for delivering a helmet-to-helmet hit on Smith in the second quarter.

Colin Kaepernick, who took over Smith’s starting job in San Francisco last season, only played the first offensive series. He threw a pair of passes with one completion for minus-3 yards.

The Chiefs played without Pro Bowl running back Jamaal Charles, who strained his right foot when he stepped on a teammate in practice Monday. Coach Andy Reid said Charles would play if he could, but the team ultimately played it safe.

Knile Davis, one of the Chiefs’ third-round draft picks, started in Charles’ place. Davis ran for 37 yards and caught three passes for 31 yards.

Colt McCoy and Scott Tolzien alternated series for the 49ers once Kaepernick left, but neither distinguished himself in the race for the No. 2 quarterback job. McCoy threw for 35 yards but also tossed an interception, while Tolzien threw for only 30 yards.

The main story line, though, was Smith facing his former team.

After leading San Francisco to the playoffs and getting off to a good start last year, he lost the top job when he got hurt. 49ers coach Jim Harbaugh stuck with Kaepernick once Smith was healthy enough to return, and then traded the former No. 1 pick to the Chiefs this past offseason.

Smith has mostly taken the high road when asked about how things went down. He even spent some time chatting amicably with Harbaugh on the field before kickoff.

Demps, who’s trying to solidify a job returning kicks for Kansas City, sent the first shock through a meager crowd at Arrowhead Stadium in the first quarter. He fielded a kickoff after the first of Dawson’s field goals, found a crease and out-ran the coverage for a touchdown.

The Chiefs haven’t had a kickoff return for a score in a regular-season game November 2009, when Charles brought one back against the Pittsburgh Steelers.

The 49ers’ special teams also shined in the third quarter, when backup linebacker Parys Haralson blocked a punt by Dustin Colquitt. Haralson recovered the ball to set up the second of Dawson’s 55-yard field goals — both of them had plenty of distance to spare.

Those were the 49ers’ only points until Daniels hit Chuck Jacobs from 14 yards out with 2:02 left in the game. They failed to convert the extra point, but the defense made the lead stand up.

Notes: Chiefs TE Travis Kelce (bruised knee) and CB Dunta Robinson (shoulder) left the game. … RT Eric Fisher, the Chiefs’ No. 1 overall pick, missed a few plays while getting his hand examined. … Four of the 49ers’ top seven draft picks didn’t play due to injuries: DE Tank Carradine (knee), TE Vance McDonald (leg), RB Marcus Lattimore (knee) and DE Quinton Dial (toe). … 49ers LT Joe Staley was in uniform after missing four recent practices with an undisclosed injury. He had returned to practice Wednesday. … Haralson also had a sack.