Playing in just their third tournament as a team, Chan and Hingis needed an hour and thirty minutes to seal the victory 7-6(4), 6-2 and claim their first title.
The pair proved more decisive in the big moments, converting each of the seven break point chances they created, and allowing the Czechs just five of their eight.
? WTA (@WTA) March 18, 2017
"A huge thanks to my partner Latisha (Yung-Jan), we're playing in our third tournament together and she helped me in the previous two to just believe in myself again," Hingis acknowledged in the trophy presentation. "I won here a couple of years ago with Sania, so to be back here on this court again and playing the final is amazing."
The unseeded Czech duo Hradecka and Siniakova are also a new pairing in 2017 - they were through to their second final in their third tournament together. Both were making their Indian Wells doubles final debut, while across the net Hingis is a two-time champion (1999 and 2015), and Chan is a former runner-up (2007).
The Czechs got off to a strong start in the opening set, taking advantage of a few slips from the No.6 seeds to open up a double break lead for 3-1 before Chan hit back from the baseline to erase one of the breaks.
? WTA (@WTA) March 19, 2017
Smart poaching at the net from Hradecka put the Czechs in the position to serve for the opening set, but Chan and Hingis broke straight back, holding firm to force a tiebreak. Hingis came away the victor in a lengthy baseline battle against Siniakova, who targeted her with the backhand before Hingis finally drew the error - and the decisive minibreak.
It all went the way of the No.6 seeds in the second set - Chan was broken early in the set but the pair were able to get it back straight away, as well as deal another two breaks of serve to reel off four straight games and serve for the match.
A trio of scrappy rallies went Chan and Hingis' way, bringing the No.6 seeds to championship point before Chan smashed a volley away to give them the victory - and their first doubles title as a pair.
? WTA (@WTA) March 19, 2017
"It felt like we got better each match and start to trust each other and know what to do on big points," Hingis said. "I mean, today, even in the first set we were sometimes back, but we came back because we knew we could come out of difficult situations."
Chan added, "For [our] first two tournaments in Middle East, we were trying. We know each other as opponent. We didn't know how to work together, and we spent a lot of time on court, off court, try to know each other and try to build up the trust between each other.
"I think those two tournaments, even though we didn't win the title or didn't get into the final, but still help us a lot. I think that's actually key. As a partner, you can't expect, once you play together, you can win the titles all the time. You still need time. Those two tournaments help us a lot here."