Stormers coach Allister Coetzee says that his players appeared to "run out of energy" in their 26-21 victory over the Rebels at Newlands in Cape Town.
The Stormers who were outscored 2-3 in tries almost lost Springbok captain Jean de Villiers before the match as he took ill but his condition stabilised and he was able to take his place in midfield.
"It was frustrating in a way because they didn't have the energy," said Coetzee.
"I'm not able to say why but we looked flat at times but this team has been able to move on and cope with adversity.
"The intensity was quite high out there today and there was so much pressure. The players felt they were getting tired.
"I salute the players because they've won the SA Conference for the second successive year and it's been tough.
"We can't take away anything from this team because it's a fantastic achievement to finish in the No 1 place on the log. It ranks as the franchise's best ever season in the history of Super Rugby.
Coetzee said his side had worked really hard and it had paid off.
"We were not happy with our performance today but for us it was always about winning, first and foremost," he said.
"We've now reached our objective of making the play-offs and, from this point on, it is about winning and playing the percentages.
"We are comfortable with the way we play and will not make changes now.
"You do not need bonus points in the semi-finals."
The Stormers' next match will be in fortnight's time and Coetzee said his squad would welcome the break.
"We will celebrate this win and then start preparing for maybe the Crusaders or may be the Bulls."
Stirling Mortlock said his team had been highly motivated and the players had taken to heart his pre-match team talk in which he appealed for all-out commitment.
"We had a desire to do well, and I'm proud of the way we played today, it was outstanding," said the Rebels' captain.
"I certainly felt we did enough to have won this game and from our perspective we were on the wrong end of a quite a few (refereeing) decisions.
"It was tough to deal with that. There were times when we thought the penalty would go our way and then it didn't.
"The Stormers' defence was outstanding and, when it comes to finals rugby, it is all about winning.
"I rate their championship chances very highly."