Webber topped the timesheets when he lapped the Montreal street circuit in his Red Bull in one minute 17.895 seconds.
The final practice had been scheduled to last an hour but officials initially delayed the start to repair a safety barrier that was damaged when a car crashed into a fence during one of the earlier support races.
They then announced that the session would be reduced to 30 minutes to comply with the sport's rules that there needed to be a two-hour break between practice and qualifying, which was due to start at 1700 GMT.
With the reduction in time and light rain falling at the Circuit Gilles Villeneuve, the teams all adopted a cautious approach before the battle for pole position.
Webber completed only seven laps and his fastest was more than three seconds slower than the best times from Friday's second session, when the track was dry.
The weather forecast for qualifying and Sunday's race remained unpredictable with more rain possible, leaving teams in a dilemma about which tyres to choose for the seventh round of this year's Formula One championship.