The home side, who extended their winning run to five matches, went in front a minute before half-time when central defender Baudry met Dean Cox's right-wing cross to send a well-placed header into the corner of the net from eight yards out.
Despite difficult conditions with a combination of driving rain and wind, there was plenty of quality from both sides but the O's increased their advantage with a sweet move started by Martin Rowlands. The midfielder flicked a pass into the path of David Mooney who shrugged off a tackle before the ball fell to Lisbie and he drove home a left-foot shot for his sixth goal of the season.
Immediately afterwards, referee Andy Davies was forced to leave the action with a calf strain and he was replaced by fourth official Michael Blackledge.
Preston, who had started the match unbeaten in seven games, enjoyed their best spell in the last 15 minutes. Substitute Akpo Sodje had been on the field for a minute when his header struck a post. From the rebound, Chris Robertson stabbed the ball goalwards only to see it cleared off the line.
Sodje met another cross late on but Orient goalkeeper Ryan Allsop clawed the ball away as the O's were forced into some desperate defending.