A confident-looking Dynamo put plenty of pressure on the home side's goal in the early stages at a packed Nou Camp but it was Messi who opened the scoring in the 25th minute.
The prolific Argentina forward, top scorer in last season's competition, made a trademark dash in from the right flank and struck a low shot that had enough power to beat Olexandr Shovkovskiy at his near post.
Barca increased the pressure after the goal and Shovkovskiy had to sprint off his line to deny Zlatan Ibrahimovic after Xavi's pass had sent the Sweden striker clear.
The Dynamo goalkeeper reacted superbly to keep out Xavi's first-time strike from a Messi centre five minutes before the break and Messi, Ibrahimovic and Daniel Alves all went close to doubling the lead.
A dominant Barca continued to press forward in the second half and the lively Ibrahimovic should have done better than head Xavi's pinpoint cross straight into Shovkovskiy's arms.
"It's great to be top because the group is terrible and we had really bad luck with the draw," he told a news conference.
"The statistics show that the champion never wins twice in a row," he added. "Everyone is gunning for you and it's easy to think you can get through with a little bit less effort and that's when you can get knocked out."
"We have lost the match but I have to recognise that they are a very good team," he told a news conference.
