Frenchman Cabaye, making his first start after a two-month injury layoff, put Newcastle ahead in the 35th minute with a superb free-kick and the home side looked on track to grab three crucial points in the battle to avoid relegation.
However, Newcastle lost their way in the second half and two goals from substitute Adam Le Fondre gave Reading a 2-1 win, their first ever victory at St James' Park.
Pardew, whose side have won just three times in 18 games since he signed an eight-year deal in September, acknowledged the boos that rained down after the Cabaye substitution but said he had no option but to replace him.
"The substitutions that were made were greeted with jeers and I have to accept that," he told the club's website after a defeat that left Newcastle just two points from the drop zone.
"One of them, Yohan, I had no choice with because he had an injury, which was something that we were worried about but fortunately it doesn't look too bad."
Cabaye was taken off in the 74th minute with the scores tied at 1-1. Three minutes later Reading were ahead and Newcastle fans vented their frustration from the stands.
Pardew said Cabaye had indicated he needed to be taken off.
"He told me about five minutes before he came off that he was injured," he told the BBC.
"Of course the players and the fans don't want to see a great player go off the pitch. It made it difficult for me because that negativity spread around the stadium and to the players. And that's what happens when you're down the bottom.
"It was a negative stadium in the second half, there were a lot of boos and the players were trying to do their best."
Pardew said he must add to the squad after seeing striker Demba Ba leave the club to join Chelsea and losing out on France forward Loic Remy, who opted to sign for bottom club Queen's Park Rangers instead of Newcastle.
Reading manager Brian McDermott was understandably thrilled with the win, his team's second come-from-behind victory in a row. Reading fought back from two down against West Bromwich Albion to win 3-2 last Saturday.
"It's a fantastic win, I don't know if we'll get the coach back or fly now - but to be honest I don't care, I'll walk home!" he told the club's website.
After winning just once in their opening 19 games in the Premier League, Reading have now won three of their last four and McDermott said his side had learned how to get results in the English top flight.
"We were losing games, high scoring games ... but we've learned from that. You have to stay in games in this division and we did that at 1-0," he added.
Reading, with 19 points, remain in the drop zone in 18th place but are just one point from safety and trail Newcastle, who finished fifth last season, by two. (Writing by Peter Rutherford in Singapore, Editing by Patrick Johnston)
- Sports & Recreation