The win took Belgium level with Austria on seven points and five points behind group leaders Germany who host Kazakhstan on Saturday and have a 100 percent record from their four games.
Austria have played four games and Belgium five.
The match was a pale shadow of the thrilling 4-4 draw the two sides served up in Brussels last October.
Witsel set Belgium on their way in the sixth minute when he broke clear of the offside trap and beat goalkeeper Jurgen Macho to the ball to head the opener.
Austria should have equalised shortly afterwards when captain Marc Janko was sent clean through but needed one touch too many and allowed Simon Mignolet to smother the ball at his feet - the only real save the Belgian goalkeeper had to make.
Austria's moves repeatedly broke down in midfield and it was no surprise when Belgium, looking more dangerous on the counter-attack, scored another five minutes after half-time.
Laurent Ciman's inswinging cross found Witsel at the far post and the 22-year-old Standard Liege player had time to chest the ball down and smash a left-foot shot past helpless Macho.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.