In Week 6 (October 11), a 7-6 loss to the Oakland Raiders, Whelihan again replaced Leaf late in the game. Leaf had thrown three interceptions, and Whelihan threw an interception in his first drive. Trailing 7-6 and on 4th-and-6 on Oakland's 38 with 42 seconds left, Whelihan completed a screen pass to Natrone Means, but Means fell six inches short of the first down. After Leaf completed only 4 of 15 passes with an interception in Week 10 (November 8), Whelihan replaced Leaf and had a better performance: 13 of 23 completed passes for 113 yards and a touchdown. San Diego lost 27-10 to defending champion and this season's eventual champion Denver Broncos. Effective Week 11 (November 15), Whelihan was starter on a permanent basis. San Diego finished 1998 5-11, just one game better than in 1997; Whelihan had a 2-5 record as starter. Both of Whelihan's wins were by one point: 14-13 over Baltimore Ravens in Week 11 and 38-37 over Kansas City Chiefs in Week 12 (November 22). In Week 11, Whelihan completed 15 of 42 passes for 172 yards and a touchdown, and Whelihan improved in the next game with 19-for-37 passing for 279 yards, 2 touchdowns, and an interception. A five-game losing streak followed those two wins. In the season finale on December 28 against the Arizona Cardinals, Arizona safety Kwamie Lassiter intercepted Whelihan four times; one of Lassiter's interceptions bounced off Chargers receiver Ryan Thelwell. With 16 seconds left on 4th-and-20, Thelwell caught a 30-yard touchdown pass from Whelihan, and the extra point tied the game at 13. However, Chris Jacke kicked the winning field goal as time expired, and Arizona's win qualified the team for the playoffs for the first time in nearly 15 years.