Bartoli, ranked 14 in the world, has now lost five times in 11 meetings against her Chinese opponent, who held firm after two one-sided sets to set up a showdown in round two against Romina Oprandi of Switzerland.
The former Wimbledon finalist from France is scratching for form after three straight first-round exits.
"The first match on clay is always tough for me and obviously at the beginning I had a lot of trouble finding my game and my feet on the court," said Bartoli afterwards.
"I wasn't feeling comfortable and Peng Shuai was playing extremely well as well. I just tried my hardest on the court and was able to play some good shots in the second set.
"It was a very difficult draw, but I think it is better for me to have those kind of matches early in the clay court season and try to improve for the big events coming up."
WTA Estoril results
Urszula Radwanska (Poland) beat 2-Dominika Cibulkova (Slovakia) 2-6 6-4 6-4
Monica Puig (Puerto Rico) beat 8-Julia Goerges (Germany) 7-6(3) 6-2
Francesca Schiavone (Italy) beat Lourdes Dominguez Lino (Spain) 6-2 4-6 6-3
Estrella Cabeza Candela (Spain) beat Aravane Rezai (France) 5-7 6-1 6-3
Kaia Kanepi (Estonia) beat Kristina Mladenovic (France) 6-4 6-3
3-Anastasia Pavlyuchenkova (Russia) beat Shahar Peer (Israel) 6-4 6-4
Romina Oprandi (Switzerland) beat Kiki Bertens (Netherlands) 6-3 6-3
Peng Shuai (China) beat 1-Marion Bartoli (France) 6-0 1-6 6-4
Galina Voskoboeva (Kazakhstan) beat Sofia Arvidsson (Sweden) 6-3 6-4
Monica Niculescu (Romania) beat Tamira Paszek (Austria) 6-1 6-3
ATP Estoril results
Gastao Elias (Portugal) beat 7-Horacio Zeballos (Argentina) 6-3 6-4
8-Tommy Robredo (Spain) beat Daniel Gimeno-Traver (Spain) 2-6 7-5 6-3
Robin Haase (Netherlands) beat Pablo Andujar (Spain) 4-6 6-2 6-3
Paolo Lorenzi (Italy) beat Niels Desein (Belgium) 6-3 4-6 6-2
Victor Hanescu (Romania) beat Rui Machado (Portugal) 6-4 6-4
Albert Ramos (Spain) beat Carlos Berlocq (Argentina) 7-6(4) 2-6 6-3
Alejandro Falla (Colombia) beat Andrey Kuznetsov (Russia) 7-5 6-4
Pablo Carreno (Spain) beat 5-Julien Benneteau (France) 6-3 6-4
ATP Munich results
Gael Monfils (France) beat 8-Jurgen Melzer (Austria) 6-3 6-3
Evgeny Korolev (Russia) beat Marcos Baghdatis (Cyprus) 7-5 7-6(3)
6-Florian Mayer (Germany) beat Lukasz Kubot (Poland) 7-6(2) 4-6 7-5
5-Alexandr Dolgopolov (Ukraine) beat Sergiy Stakhovsky (Ukraine) 6-4 6-2
Viktor Troicki (Serbia) beat Matthias Bachinger (Germany) 6-3 6-2
Radek Stepanek (Czech Republic) beat 7-Mikhail Youzhny (Russia) 6-4 5-7 6-4
Grega Zemlja (Slovenia) beat John Millman (Australia) 6-2 6-2
Ernests Gulbis (Latvia) beat Jarkko Nieminen (Finland) 6-4 6-2