The Estonian, who had a first-round bye, was broken once in the first set and twice in the second in her first match on the surface for almost a year.
Rodionova, who had had two matches in qualifying, advanced to the round of 16 against 2009 champion Magdalena Rybarikova after the 14th-seeded Slovakian beat Coco Vandeweghe of South Africa 6-2, 6-1.
Kanepi says "I didn't have any rhythm at all and she played very well."
Mirjana Lukic defeated the only other seeded player to lose, saving a match point to win 6-7 (2), 7-6 (4), 7-5 against No. 5 Roberta Vinci of Italy.
Results on Tuesday at the Aegon Classic:
Singles
Second Round
(Q) Arina Rodionova (RUS) d. (1) Kaia Kanepi (EST) 64 62
Mirjana Lucic (CRO) d. (5) Roberta Vinci (ITA) 67(2) 76(4) 75
(8) Aravane Rezai (FRA) d. Olga Govortsova (BLR) 75 ret. (left ankle sprain)
(14) Magdalena Rybarikova (SVK) d. Coco Vandeweghe (USA) 62 61
Singles
First Round
(9) Ayumi Morita (JPN) d. (Q) Ajla Tomljanovic (CRO) 63 36 76(4)
(11) Yaroslava Shvedova (KAZ) d. Zheng Jie (CHN) 62 76(5)
Christina McHale (USA) d. Anastasia Rodionova (AUS) 36 76(7) 62
Tamira Paszek (AUT) d. Sania Mirza (IND) 63 46 62
Andrea Hlavackova (CZE) d. Jill Craybas (USA) 63 61
Misaki Doi (JPN) d. Edina Gallovits-Hall (ROU) 64 62
Casey Dellacqua (AUS) d. Sandra Zahlavova (CZE) 75 76(5)
(Q) Naomi Broady (GBR) d. Caroline Garcia (FRA) 62 67(5) 64
Other results from the e-Boks Sony Ericsson Open:
Singles
First Round
(1) Caroline Wozniacki (DEN) d. Irina Falconi (USA) 62 63
(4) Lucie Safarova (CZE) d. (Q) Johanna Konta (AUS) 46 75 63
(5) Barbora Zahlavova Strycova (CZE) d. Sofia Arvidsson (SWE) 62 61
Simona Halep (ROU) d. (6) Anastasija Sevastova (LAT) 67(5) 76(4) 60
(Q) Galina Voskoboeva (KAZ) d. (7) Jelena Dokic (AUS) 63 61
Johanna Larsson (SWE) d. Vesna Dolonts (RUS) 63 63
Zhang Shuai (CHN) d. (WC) Julia Boserup (USA) 62 63
Michaella Krajicek (NED) d. Melanie Oudin (USA) 61 75
(Q) Mona Barthel (GER) d. (Q) Alexa Glatch (USA) 62 75