Having signed for Orient a month ago from MK Dons, MacDonald opened his account for the east Londoners at the seven attempt with a typical predatory striker's goal.
Dean Cox sent in a free-kick from the left and MacDonald's header from point-blank range was parried by goalkeeper Owain Fon Williams but the 31-year-old nodded the rebound into the net.
Rowlands had the chance to double the lead six minutes later but saw his 15th-minute penalty well-struck saved after Cox had been fouled by Ash Taylor.
However, the midfielder made amends after 67 minutes. He pounced on a clearance 25 yards from goal and struck a dipping, left-foot volley to the left of Williams that gave the keeper no chance.
Tranmere gave themselves a lifeline when substitute Michael O'Halloran arrived at the far post after 75 minutes to sweep in a cross from Danny Holmes but the home side were good value for their victory.