The Bayern Munich striker fell to the ground after almost being hit by the projectile, which had been thrown from a section of the home supporters.
The incident forced the referee, Slovenia’s Damir Skomina, to stop play for several minutes in the second half.
Skomina had already halted proceedings briefly before the break after flares and firecrackers were thrown onto the pitch.
Lewandowski recovered from the scare to score his side’s final two goals.The 28-year-old striker applied a cool finish to double Poland's lead in the 82nd minute, before converting a penalty in stoppage time.
Kamil Grosicki, the Rennes winger, had initially given put the visitors ahead at Bucharest’s Stadionul National with an excellent solo effort, dribbling past five Romanian defenders before scoring.
The win, which had also seen play briefly suspended in the first half after firecrackers were thrown onto the pitch, saw Adam Nawalka’s Poland top Group E with 10 points from four games.Reuse content