Niners quarterback Brock Purdy threw for three touchdowns and 255 passing yards with no interceptions, while Deebo Samuel made three receptions for 102 yards and a touchdown.
San Francisco, who in recent weeks have struggled to close out wins when leading, looked poised to buck that trend with something to spare after surging into a 23-3 lead early in the third quarter at Lumen Field after touchdowns from Samuel and Kittle and three Matthew Wright field goals.
But the Seahawks came roaring back with a sensational 97-yard kick-off return into the end zone from Laviska Shenault Jr. to inject fresh belief into the home side's challenge.
After forcing a stop on the next 49ers possession, Seahawks quarterback Geno Smith marched his team 94 yards upfield on a 13-play drive which ended with running back Kenneth Walker blasting over for a touchdown from one yard out to help make it 23-17.
Yet the Seahawks' rally faltered midway through the fourth quarter, when 49ers cornerback Renardo Green picked off Smith as he attempted to find D.K. Metcalf.
That left the 49ers in prime field position at the Seattle 15-yard line, and from there Purdy made no mistake, finding tight end Kittle with a nine-yard pass for the touchdown, extending San Francisco's lead to 29-17.
Seattle refused to throw in the towel though and set up a nervy finale with one minute and 44 seconds remaining after Smith connected with Tyler Lockett in the end zone for a touchdown that left the Seahawks within five of the lead.
Any hopes of a Seattle miracle, however, were snuffed out on the opening San Francisco possession after the restart.
Rookie running back Isaac Guerendo burst clear from the line of scrimmage on a 76-yard run before stopping short of the goal line.
From there fullback Kyle Juszczyk rumbled over from six yards to make the game safe.
The 49ers improved to 3-3 with the win and now lead the NFC West while Seattle fell to 3-3.
