An own goal from a corner kick that deflected off Jordanian defender Yazan Al Arab gave Austria a 2-1 lead in the 76th minute. Marko Arnautovic's penalty kick deep in stoppage team extended the margin on Tuesday.
The game between a Jordanian team on debut and an Austrian squad back on soccer's biggest stage after missing the last six tournaments featured plenty of excitement.
It peaked in a stretch in the second half that featured an equaliser by Jordan and two balls sent into the net off corner kicks by Austria, with only one of those counting.
The 37-year-old Arnautovic, who came on as a substitute in his World Cup debut, had appeared to give Austria the lead when he converted from a corner kick after an error from Jordanian goalkeeper Yazeed Abulaila.
But the decision went to VAR and the referee called a hand ball on Stefan Posch whose arm had touched the ball in the lead up.
Austria got another corner kick shortly after the second-half hydration break and took a 2-1 lead on Al Arab's own goal.
That proved to be the difference for Austria, who earned their first win at the World Cup since beating the United States in a group-stage match in 1990.
Jordan fell short in their attempt to become the first country to win in their World Cup debut game since Senegal managed the feat in 2002 against defending champions France.
Romano Schmid scored in the 20th minute for Austria when he capped off an impressive buildup that put the Jordanian defence on their heels.
Xaver Schlager fed a pass to Schmid, who hit a perfectly struck right-foot shot from the edge of the area into the top corner of the net.
Ali Olwan drew matters level for Jordan in the 50th when he made a long run into the box on a counterattack and beat Alexander Schlager with a right-foot shot that delighted the large contingent of Jordanian fans.
Jordan will return to Santa Clara for their second match next Monday against Algeria, who lost 3-0 to Argentina in the first Group J match.
Austria will face Lionel Messi and Argentina in Dallas that same day.
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