Cowan tore a ligament in his ankle at training on Thursday and it was doubtful he would play against the Bulls.
But thanks to the Highlanders' medical team, Cowan made it on to the field to put in an inspirational performance.
Though he would not admit to it, his ability to play was helped by a pain-killing injection before the game.
Cowan said the side had shown some real backbone and "everyone was up for it".
"The guys showed huge ticker out there. We've got the bye next week so I said to them before the game to leave no stone unturned out there tonight, and throw everything at them," Cowan said.
"We've got these young fellas in the team who are starting to believe in themselves.
We've got the right management and right structure and if these guys start believing in themselves then we can knock over anyone."
Cowan said the plan was to get in behind the Bulls, and the South Africans played a compressed defence so there were always going to be holes in behind them.
"The Bulls play a sort of bully game and once they start getting physical with you they grow from that. But we really got into them at the breakdown, and rose to the challenge."
Adam Thomson and Alando Soakai were dominant at the breakdown.
Thomson said it was something the side had targeted.
"We had a good look at them this week and we knew they were good runners, but they tended to isolate themselves.
"We knew if we knocked them over around the legs and got in and contested that ball we would get a few turnovers, and we did," Thomson said.
Thomson had a top game, featuring more on attack, which he said was something he had been trying to do in the past couple of weeks.
"It's just the way the game has been going. I've just been concentrating on being more physical in the breakdown and in the tackle and then the game will loosen up later on."
The Highlanders have next week off with the bye, which Thomson said was well placed in the middle of the competition.
Highlanders coach Glenn Moore said the side had built momentum over the past couple of weeks and that had paid off on Saturday night.
"I don't know what the statistics were but we were really aggressive at the breakdown and got a lot of turnovers," Moore said.
"We knew these guys would want to bash us around but I had no doubts we'd be up for the confrontation side of it.
"We sent a message out halfway through the first half [that] we could see some holes appearing, and we just needed to be direct and when the holes appeared we had to run straight at them, and that is when the tries came."
Moore said Cowan was outstanding in all areas.
"He was very lucky to play today. Most people would not have played today, but not Jimmy. Not only did he play but he played very, very well and showed a lot of backbone.
"We knew we had to meet their physicality. We wanted to get into them and counter-ruck them and we did that."
Moore praised the set-piece and said he was happy to now have the bye as it was a chance to rest some bruised bodies.
Bulls coach Frans Ludeke said his side had lost the match at the breakdown.
"They deserved to win. We were just not good enough, especially at the breakdown," he said.
"You never see things like this coming. We just could not get going, get any momentum."
