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.
He made amends in the 76th minute when he released Pedro, who replaced Andres Iniesta at halftime, and the 22-year-old sent a precise shot into the bottom left corner.
The win put Barca top of Group F on four points from two matches after 10-man Inter Milan were held to a 1-1 draw at Rubin Kazan earlier on Tuesday. Dynamo are second with three points and Inter third on two.
TERRIBLE GROUP
Barca coach Pep Guardiola paid tribute to a superb defensive performance from captain Carles Puyol and said three more points at home to Rubin next month would be a significant step towards qualification for the knockout phase.
"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."
Dynamo striker Andriy Shevchenko, back at his original club after spells in Italy and England, scored a first-half hat-trick in a 4-0 thrashing of Barca at the Nou Camp in the 1997-98 season but there was to be no repeat on Tuesday.
The former AC Milan and Chelsea man, who was celebrating his 33rd birthday, blazed one shot over the bar in the early stages but laboured on his own up front for most of the match.
Dynamo coach Valery Gazzayev said his side had tried to catch Barca on the counter-attack but the strategy had failed.
"We have lost the match but I have to recognise that they are a very good team," he told a news conference.
