Sir Roger, also chairman of Scottish Gas owner Centrica, called for British companies to "redouble" their exporting efforts as they seek to make their way through the economic downturn and highlighted that for the first time in 40 years Britain is a net exporter.
"Businessmen and politicians must keep a bridge to Europe firmly in place," Sir Roger said.
He added Britain must "avoid the real risks of isolation".
"Europe is the bedrock of our international trade. It should be regarded as the launch pad from which our global trade can expand, not a landmass from which we should retreat," he said.
The CBI's warning comes as Prime Minister David Cameron prepares to participate in EU budget talks this week.
He has threatened to use the UK's veto if the rise proposed by the European Commission is not cut.
Meanwhile Mr Cameron is facing increasing pressure from within his own Conservative Party to negotiate a looser relationship with the rest of the Union, with some demanding a referendum on withdrawal.
Sir Roger said: "Politicians must engage, corners must be fought and battles must be won for this country but the cold business logic of a European partnership out of self-interest must be argued for and ultimately must prevail."
Britain's relationship with Europe was a key theme of the conference with Labour Party leader Ed Miliband using his conference speech to warn Britain is "sleepwalking" into leaving the EU, which could leave it "voiceless and powerless".
He warned that outside the EU, the UK would simply be an "offshore, low- value-added, low-wage Britain".
However, Mr Cameron told the audience: "I make absolutely no apology for standing up for Britain in Europe, for some of our priorities."
He added: "I do not think it makes you a bad European because you want a tough budget settlement in Europe."
He claimed to have the backing of the people of Europe in seeking spending cuts in the EU institutions.