Hadden saw his side score three tries, through Nikki Walker, Sean Lamont and Glasgow's Euan Murray at the Stade de France.
But they could not suppress the French, who went over six times themselves to all but seal their fourth RBS 6 Nations Championship in six years.
"We are disappointed with the result," he said. "We came here to win, although the better side won on the day.
"We had very relatively little to play for in this game, but we put in a gutsy performance. We ran out of steam, though, in the second half.
"Some of the French scores were fortunate but they deserved to win and to win the championship."
Hadden was happy with his side's tournament as a whole, even though they finished with a 1-4 record in the end.
"Before the start of the Six Nations, we had 14 injuries and everyone thought we were in disarray," he added.
"We ended up coming here disappointed we did not have a chance to win the title.
"We should have won our last two home games (against Italy and Ireland) and that would have given us a chance of winning the tournament."
Scotland decided not to kick for goal three times in the dying stages, preferring instead to go for tries.
They ended up going over, through Euan Murray, just before the start of injury time.
Knocking over all the penalties on offer, however, could have ruined the title hopes of France, who needed to win by 24 points to overtake Ireland in the table.
Captain Chris Paterson does not regret the strategy adopted by his side.
"We just concentrated on ourselves," said the full-back, who booted four points on the day.
"I was unaware how many points France needed to score. I was just thinking about the development of our team.
"We wanted to score tries for the benefit of the Scottish team."
Elvis Vermeulen scored the winning try for the French deep into injury time, although it needed the say-so of the video referee before it was awarded.
Paterson added: "I didn't see the grounding. One or two of our guys thought they had got the hands under the ball.
"The referee said he was sure it was a try so we accept it."