And winger Chris Burke was forced off with a rib injury, while others played despite suffering from a virus.
"We will have a head count and see how everybody is," said Jones ahead of Tuesday's FA Cup clash at Bristol City.
"I've got three or four lads in there throwing up who could have easily come off, but the likes of Kevin McNaughton stayed on. Ross McCormack couldn't as he's not too good.
"We've got Burkey with a rib injury, Josh who's picked up a broken leg and Jay (Bothroyd) down with illness.
"Also we've got Joe (Ledley) carrying on with his hip injury, and Gavin (Rae) since he broke his hand, he's only had two days training."
Jones' biggest blow was the injury to 19-year-old Magennis who enjoyed a lively 35 minutes of his first Championship start before being forced off after a 50/50 challenge.
Magennis was given the nod to start ahead of top scorer Michael Chopra who was on the bench after Bothroyd was earlier ruled out through illness.
"It's heartbreaking for Josh," said Jones. "We really feel for him.
"With Jay unavailable, I'd picked him to give us some height up front against the big Blackpool defenders and he was doing really well.
Cardiff City manager Dave Jones
"He felt something crack. It was a poor challenge. We've got the video evidence and the referee hasn't.
"He's made the decision and given a throw-in to us which seemed a little bit harsh at the time."
The latest setbacks add to what has already been a turbulent week for the Bluebirds who face a second winding up order over an unpaid debt to Her Majesty's Revenue and Customs, reported to be £2.7m.
But Cardiff remain fourth in the Championship despite Blackpool's Charlie Adam cancelling out Mark Hudson's first half opener.
Now their attentions turn to the FA Cup on Tuesday for their rearranged third-round clash at Bristol City which was postponed a week ago because of a frozen pitch at Ashton Gate.
And Jones is hoping his suffering stars put up the same fight they did on Saturday.
"At the moment we have this viral going around the club and we will just have to see how they are," he said.
"I think the lads did as much as they possibly could. I'm proud of them because they had to dig deep."
Source: BBC Sport
Source: BBC Sport