John McGynn’s men were on the receiving end for most of the game and were reduced to 10 men on the hour when Christophe Berra was shown an automatic red card for an apparent high tackle on Cammy Smith.
Thistle were worthy of their victory but Rovers showed plenty of robust defending during a game where effort was high but visibility was low.
"The guys battled so hard, they defended so well with 10 men for half an hour – Christophe Berra is such a key player for us,” he said.
McGlynn added the veteran centre back had withdrawn from the tackle and the conditions made it very difficult to see the players when the incident was watched back.
"It’s the end of a very, very good run, so we just need to start a new one,” he said. “Enormous credit to the players who have done so well to get us into that 15-game unbeaten run – we nearly made it 16.
"A massive thank-you to our fans today, who backed us enormously throughout the whole game. When we lost, they appreciated the effort the players put in.”
"Deep down, I can hardly deny Thistle their win – they were the team creating the chances. I can’t deny they deserved to win but I am gutted for our players, who put so much into the game.”
Kyle Benedictus and Aaron Arnott both stepped up from last week’s bench to the starting XI, while Tom Lang and Ethon Varian took a step back. There was also no room among the subs on the day for Matej Poplatnik or Blaise Riley-Snow, with Greig Young named among the replacements.
The home side started the stronger and had a couple of early half-chances, with Smith, Stuart Bannigan and Richard Foster linking well to create openings from midfield and get crosses into the Raith box.
Rovers strung together a few moves of their own around the quarter-hour mark, with Dario Zanatta and Aaron Arnott aiming to flight the ball into the danger area after a burst of pressure.
Raith continued to live dangerously, however, surviving appeals for a penalty when Brian Graham got behind his marker but went down on the box, a magnificent tip over the bar by Jamie MacDonald from a Ross Docherty header, a cross from Smith which grazed the post and a close-range shot from Kevin Holt which flew wide.
Zanatta went into referee Steven Kirkland’s book on the half hour for hauling back Smith on the right flank after his opposite number had gone past him.
Thistle turned up the heat again towards half time and had several good opportunities in front of goal but couldn’t find the final touch.
As usual, Rovers had defenders back when it mattered but they were fortunate to reach the interval on level terms, especially after the flurry of Partick chances midway through the first half.
Three minutes into the second half, Reghan Tumilty almost put his team in trouble by heading the ball to Zak Rudden but Christophe Berra was there to mop up.
After 56 minutes, Raith’s Arnott crossed after a lay-off from Tumilty but no one was there to provide a friendly touch.
On the hour came the flashpoint, with Berra shown a straight red card for a seemingly high-booted challenge on Smith in midfield.
Frankie Musonda replaced Zanatta for Raith soon afterwards, while Thistle’s Kyle Turner took over from Thistle’s Ruddon.
MacDonald made another outstanding close-range save from Turner moments later.
The closing minutes saw Thistle continue to try to break the deadlock, with a couple of good efforts ballooned over the bar – including yet another by Turner – while Mitchell was a late Raith replacement for Ethan Ross.
Then Turner finally found the target with that deadening blow for Rovers, after more than five minutes of stoppage time had been played.
He lashed the ball home from inside the area when sub Ross MacIver headed it down into his path, following a cross from the left by Scott Tiffoney.
Partick Thistle: Sneddon, Foster, Holt, Mayo, Tiffoney, Bannigan, Graham, Ruddon (Turner 64), Smith (MacIver 72), Akinola, Docherty. Subs not used – Stone, Gordon, McKenna, Hastie, Hendrie.
Raith Rovers: MacDonald, Tumilty, Dick, Berra, Benedictus, Connolly (Young 90), Matthews, Zanatta (Musonda 64), Tait, Ross (Mitchell 80), Arnott. Sub not used – Thomson.
Referee: Steven Kirkland.