The world No. 5 made 26 unforced errors in the match, which cost her not only the chance to win the title but also to move up to the No. 3 in world ranking.
Lesia Tsurenko could not complete another upset and was beaten by Karolina Pliskova in Sunday's Brisbane International final.
"Donna's a tough opponent, so I knew I had to improve from last night", she said, referring to her 6-1 1-6 6-1 defeat of Australian Ajla Tomjlanovic. But then the ball wouldn't go in and then I would go back to being childish and stuff.
Former finalist Sam Stosur made an impressive start to the tournament as she came from a set down to beat Dominika Cibulkova 3-6 6-3 6-4 - the first time the pair had contested three sets in a match.
Of course I tried, but I felt so far away from playing good tennis.
The Ukranian world No. 27 had not lost a set in reaching her first top-level final and handled the nerves well when ousting favourite Naomi Osaka in the semi-finals.
"I was just focused on every point and thinking about every shot like it's the most important one".
But Nishikori, who had lost nine consecutive ATP finals over 52 tournaments in almost three years, broke the Russian player's serve on four consecutive points in the final game to clinch the match in just 2 hours, 6 minutes, at Pat Rafter Arena.
"Last year I did a lot of that and I'm trying to change it more, and I think I have, towards the end of last year".
He only served two aces compared with the 11 sent down by Chardy, but Nishikori returned superbly and pressured the Frenchman's serve throughout, breaking him twice in each set.
He also moved around the court well, his speed not noticeably affected by the injuries that hampered him a year ago.
"I think everything was against me today".
"Everything was working well today", Nishikori said. "But, yeah, I feel like today was a very valuable lesson".
"Physically and tennis-wise I think it was ideal".