Novak connected from 32, 24, 31 and 43 yards for the Texans.
Cairo Santos made three field goals in the fourth quarter to cut the lead to 19-12, but Houston recovered the onside kick with less than a minute left to seal the victory.
The Texans (2-0) showed that they are a much different team than the one that was embarrassed in a 30-0 wild-card playoff loss to the Chiefs (1-1) in January, when quarterback Brian Hoyer had five turnovers.
New quarterback Brock Osweiler did throw two interceptions but the Chiefs had more trouble taking care of the ball, with Houston's defense setting a franchise record by recovering three fumbles in the first half.
The first came when a high snap sailed over Alex Smith's head. J.J. Watt shoved him out of the way with one hand and pounced on it, showing he was getting back to his old self after July back surgery.
Osweiler, who finished with 268 yards passing, connected with Hopkins on a 27-yard touchdown pass on the next play to make it 7-0.
Watt continued to shine later in the first quarter when he took Smith down for his first sack this season, forcing the Chiefs to kick a field goal that made it 7-3.
Houston was leading by seven in the second quarter when Spencer Ware fumbled, Kevin Johnson scooped it up for his first career recovery and returned it 52 yards. The Texans couldn't get their offense going after that and settled for a 24-yard field goal to make it 13-3.
John Simon forced the last fumble of the half on his strip-sack of Smith. It was recovered by Whitney Mercilus. But once again Houston failed to move the ball and Novak's try for a 57-yard field goal fell short as time expired in the first half.
Marcus Peters intercepted Osweiler at the goal line on Houston's first possession and picked him off again late in the third quarter.
That led to a 43-yard field goal that cut the lead to 13-6.
A field goal by both teams after that left the Texans up 16-9.
Houston rookie receiver Will Fuller finished with four receptions for 104 yards to become the first rookie in franchise history with consecutive 100-yard receiving games to start his career. The 21st overall pick in this year's draft had 107 yards receiving in his NFL debut last week.
Houston rookie WR Braxton Miller injured his hamstring in the first half and did not return.
Watt finished with 1.5 sacks on Sunday to give him 76 sacks in his 82nd career game. He's the second fastest in NFL history to reach 75 sacks behind Hall of Famer Reggie White who did it in 65 games.
NO, NO, NO:
Peters learned that wagging your finger in the face of an opponent like NBA Hall of Famer Dikembe Mutombo did after blocking a shot is frowned upon on the NFL.
Peters forced an incompletion on a deep ball thrown to Fuller in the second quarter and wagged his finger at him for several seconds. The move earned him a 15-yard penalty for taunting and a warning that a second such penalty would result in an ejection.
SPREADING THE WEALTH:
Hopkins and Fuller gave Houston two players with at least 100 yards receiving for the eighth time in franchise history and the first time since 2013.
BRING IT BACK:
Kansas City rookie Tyreek Hill had a 105-yard kickoff return for a touchdown negated because of a holding penalty late in the fourth quarter.