Playing her first match since winning the Australian Open last month, top seed Li was pushed to three sets by Magdalena Rybarikova but eventually eased past the Slovak to post a 6-1 5-7 6-2 victory.
The Chinese world number three will next meet Petra Cetkovska who saw off Li's compatriot Zhang Shuai 6-3 4-6 6-3.
Second seeded Radwanska's path to the last 16 was slightly more straightforward after the Pole raced through the second set of her match against Sorana Cirstea to win 7-5 6-0 and set up a date with Mirjana Lucic-Baroni, a 6-4 6-1 winner over Anastasia Pavlyuchenkova.
Radwanska, a semi-finalist at this year's opening Grand Slam in Melbourne, won 70 per cent of points in the second set.
Jelena Jankovic, Angelique Kerber and Simona Halep joined the procession of seeds through to the third round, but there was disappointment for Caroline Wozniacki - who rounded off the top tier of seeded players in eighth - and second-tier seeds Ana Ivanovic and Sam Stosur.
Qatar Open results
2-Agnieszka Radwanska (Poland) beat Sorana Cirstea (Romania) 7-5 6-0
Yanina Wickmayer (Belgium) beat 8-Caroline Wozniacki (Denmark) 6-4 7-5
7-Simona Halep (Romania) beat Kaia Kanepi (Estonia) 6-4 3-6 7-6(5)
Jana Cepelova (Slovakia) beat 12-Samantha Stosur (Australia) 6-4 4-6 6-1
Monica Niculescu (Romania) beat Bethanie Mattek-Sands (U.S.) 6-1 3-6 6-3
Lucie Safarova (Czech Republic) beat Peng Shuai (China) 6-2 5-7 6-4
5-Jelena Jankovic (Serbia) beat Karin Knapp (Italy) 6-0 6-2
Klara Zakopalova (Czech Republic) beat 9-Ana Ivanovic (Serbia) 4-6 6-1 6-3
6-Angelique Kerber (Germany) beat Karolina Pliskova (Czech Republic) 7-6(2) 6-4
Mirjana Lucic-Baroni (Croatia) beat Anastasia Pavlyuchenkova (Russia) 6-4 6-1
Annika Beck (Germany) beat Tsvetana Pironkova (Bulgaria) 6-7(5) 6-2 6-2
1-Li Na (China) beat Magdalena Rybarikova (Slovakia) 6-1 5-7 6-2
Alisa Kleybanova (Russia) beat Stefanie Voegele (Switzerland) 6-3 6-2
4-Sara Errani (Italy) beat Hsieh Su-Wei (Taiwan) 6-0 6-4