Chad Henne threw two first half touchdown passes and wide receiver Ace Sanders tossed another on a trick play early in the second half to help the Jags open up a 24-10 lead.
Looking for a spark, the Texans pulled starting quarterback Case Keenum and sent in deposed veteran Matt Schaub, immediately seeing dividends with a 76-yard drive for a touchdown.
But despite moving the team into great field position twice more, Schaub and Houston could only manage a field goal, eventually falling seven points short when the home side added a late field goal.
Schaub was presented with the ball and a chance to be the hero with just over two minutes remaining and four points seperating the teams but threw an interception on just the second play of the drive.
Jacksonville (4-9) won for the fourth time in five games after starting the season with eight straight losses.
"Our guys just really believe right now," Jaguars coach Gus Bradley said.
"To come out to finish in the second half it's quite a tribute to them.
"The biggest challenge will be to keep doing what we are doing. To stay convicted in our process and stay true to who we are and what we've become."
The Texans (2-11) were hamstrung by severe ill discipline and hammered with 14 penalties for 177 yards.
The Jaguars came out firing on all cylinders and Henne went 80 yards in the opening drive in just over six minutes, culminating in a one-yard touchdown pass to tight end Marcedes Lewis.
Henne also found Cecil Shorts from six yards early in the second quarter to get a 14-0 jump.
Keenum found Keshawn Martin inside the final two minutes of the half for the Texans but a Josh Scobee field goal left the Jags leading 17-7 at the break.
Henne finished 12 of 27 for 117 yards and the two touchdowns, Schaub was 17 of 29 for 198 yards with a touchdown and interception and Keenum 16 of 29 for 159 yards with a touchdown and an interception.
Maurice Jones-Drew rushed for 103 yards for the Jaguars while Andre Johnson's 154 yards receiving was a rare bright light for Houston.