The visitors started the brightest and after only three minutes Kenny Arthur had to save a Brian Fairbairn shot from 18 yards.
Thistle hit back and on eight minutes had their fans cheering when it appeared that Paul Ritchie's close-range shot had hit the net, however it was the side netting.
After this bright opening the game lulled until 20 minutes had passed when a Mark Crilly free-kick caused confusion in the home defence, with David Craig almost netting at the wrong end.
Thistle took the lead after 34 minutes when Stephen McConalogue took advantage of a poor defensive header by Iain Davidson to lob the visitors' keeper from fully 25 yards.
Two minutes later Thistle almost doubled their lead when Billy Gibson flashed in a 16-yard shot, which appeared goalbound but was deflected for a corner.
Raith brought on Pat Clarke at half-time but the change had little effect on the flow of the match and it was Thistle who looked more likely to add to the scoring, with McConalogue going close and Craig heading over.
The visitors did hit back and on 63 minutes Paul McManus should have done better than see his overhead kick fly well over the bar.
Nine minutes later Todd Lumsden should have found an equaliser when his header from 10 yards was touched round the post for a corner.
With time running out Thistle almost doubled their lead with the last chance of the game on 83 minutes, when Scott McCulloch could only watch his 30-yard screamer be brilliantly saved by Brown in the Raith goal.
Thistle held on to record their second win in three days as they continue their push for promotion, but Raith's lack of a cutting edge is becoming a real worry.