Gloucester full-back Olly Morgan and visiting wing Richard Haughton got the only tries of the Guinness Premiership match for their sides but it was the breakdown area which frustrated both Australian Jones and home head coach Dean Ryan.
The Saracens boss, though, had a few other matters to air following the game and, speaking about Borthwick's absence, said: "I think it is ridiculous that you don't have your best English players playing in the Premiership."
All other clubs were also ordered to rest their England internationals ahead of the RBS 6 Nations, but Jones added: "It is almost a contradiction. You should have your best players playing.
"His (Borthwick's) presence in the line-out would have made a difference."
He added: "There is something wrong with the rules. The game is very difficult to referee.
"I'm not blaming the referee but it is too difficult to referee and there is so much contest at the breakdown that other things are being missed.
"The best side won today but there was no rugby played and everyone wants to see rugby.
"We have to have officials out there who want to referee but the IRB have made the laws so difficult for referees to referee and the game is immeasurably worse than it was 12 months ago.
"The referees have not got worse and neither have the players. So what's the one missing? The ELVs (experimental law variations).
"They (the ELVs) have stuffed the game up and it is very hard to play rugby."
Jones called the laws 'Rafferty Rules' - an Australian saying for an unruly person.
He added: "Nick de Kock was late tackled by a bloke, one touch-judge ran on and the touch-judge in front of him did not see it.
"There is something wrong here. We got our half-back punched and the touch-judge came on and there was no sin-bin.
"You have got to have a game where you attack off your ball and off the opposition ball. I'm as frustrated as anyone. I want to play rugby and we can't."
Ryan was also frustrated by the loss of England winger Lesley Vainikolo, who has damaged his Achilles - with the extent of it due to be discovered on Monday.
Ryan explained: "I'm disappointed at the breakdown and we went and won the game in the last half-hour.
"Les has an Achillies injury which we will have to wait to see the extent of it. He slipped. We get injuries every week and he got one this week."
Ryan also acknowledged the contribution of Mike Tindall, adding: "I think he has been strong in the last couple of weeks around the gain line and his defence was outstanding today.
"He is growing in confidence with Olly (Barkley) and whether or not (he will return to the international fold) is someone else's decision."